[English] 日本語
Yorodumi
- EMDB-16566: 70S-PHIKZ014 PHIKZ phage protein occupied ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16566
Title70S-PHIKZ014 PHIKZ phage protein occupied ribosome
Map data
Sample
  • Complex: 70S-PHIKZ014 PHIKZ phage hijacked ribosome
    • Protein or peptide: x 49 types
    • RNA: x 4 types
  • Ligand: x 1 types
KeywordsPHIKZ / Phage / hijacked / bacterial / Pseudomonas / PHIKZ014 / ribosome / 5S rRNA
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L28/L24 / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19
Similarity search - Domain/homology
Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL34 / PHIKZ014 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 ...Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL34 / PHIKZ014 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36A / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS21
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1H2O (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria) / Pseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGerovac M / Vogel J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Microbiol / Year: 2024
Title: Phage proteins target and co-opt host ribosomes immediately upon infection.
Authors: Milan Gerovac / Kotaro Chihara / Laura Wicke / Bettina Böttcher / Rob Lavigne / Jörg Vogel /
Abstract: Bacteriophages must seize control of the host gene expression machinery to replicate. To bypass bacterial anti-phage defence systems, this host takeover occurs immediately upon infection. A general ...Bacteriophages must seize control of the host gene expression machinery to replicate. To bypass bacterial anti-phage defence systems, this host takeover occurs immediately upon infection. A general understanding of phage mechanisms for immediate targeting of host transcription and translation processes is lacking. Here we introduce an integrative high-throughput approach to uncover phage-encoded proteins that target the gene expression machinery of Pseudomonas aeruginosa immediately upon infection with the jumbo phage ΦKZ. By integrating biochemical, genetic and structural analyses, we identify an abundant and conserved phage factor ΦKZ014 that targets the large ribosomal subunit by binding the 5S ribosomal RNA, and rapidly promotes replication in several clinical isolates. ΦKZ014 is among the earliest ΦKZ proteins expressed after infection and remains bound to ribosomes during the entire translation cycle. Our study provides a strategy to decipher molecular components of phage-mediated host takeover and argues that phage genomes represent an untapped discovery space for proteins that modulate the host gene expression machinery.
History
DepositionJan 29, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16566.png

Downloads & links

-
Map

FileDownload / File: emd_16566.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 544.512 Å		1.06 Å/pix.
x 512 pix.
= 544.512 Å		1.06 Å/pix.
x 512 pix.
= 544.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.46
Minimum - Maximum-7.772966 - 26.119879000000001
Average (Standard dev.)-0.008278823 (±0.89418745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 544.512 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: 70S-PHIKZ014 focused

Fileemd_16566_additional_1.map
Annotation70S-PHIKZ014 focused
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: 70S-tRNA(E)-PHIKZ014

Fileemd_16566_additional_2.map
Annotation70S-tRNA(E)-PHIKZ014
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16566_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: 70S-tRNA(P)-PHIKZ014

Fileemd_16566_half_map_2.map
Annotation70S-tRNA(P)-PHIKZ014
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : 70S-PHIKZ014 PHIKZ phage hijacked ribosome

EntireName: 70S-PHIKZ014 PHIKZ phage hijacked ribosome
Components
  • Complex: 70S-PHIKZ014 PHIKZ phage hijacked ribosome
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • RNA: 23S rRNA23S ribosomal RNA
    • RNA: 5S rRNA5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • RNA: tRNATransfer RNA
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L9
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L31
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • RNA: 16S rRNA
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S8
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S16
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S18
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S20
    • Protein or peptide: 30S ribosomal protein S21
    • Protein or peptide: PHIKZ014
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: 70S-PHIKZ014 PHIKZ phage hijacked ribosome

SupramoleculeName: 70S-PHIKZ014 PHIKZ phage hijacked ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#53
Source (natural)Organism: Pseudomonas aeruginosa PAO1H2O (bacteria)

+
Macromolecule #1: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 6.807571 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MAVQQNKKSR SARDMRRSHD ALESNALSVE KSTGEVHLRH HVSPDGFYRG RKVVDKGSDE

UniProtKB: Large ribosomal subunit protein bL32

+
Macromolecule #2: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 5.226309 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MKRTFQPSTL KRARVHGFRA RMATKNGRQV LSRRRAKGRK RLTV

UniProtKB: Large ribosomal subunit protein bL34

+
Macromolecule #3: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1
Molecular weightTheoretical: 7.387996 KDa
SequenceString:
MPKMKTKSGA AKRFKKTAGG LKHKHAFKSH ILTKMTTKRK RQLRGTSMLN KSDVARVERS LRLR

UniProtKB: Large ribosomal subunit protein bL35

+
Macromolecule #4: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 4.447445 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MKVRASVKKL CRNCKIIRRD GIVRVICSAE PRHKQRQG

UniProtKB: Large ribosomal subunit protein bL36A

+
Macromolecule #7: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 29.641256 KDa
SequenceString: MAIVKCKPTS AGRRFVVKVV NQELHKGAPY APLLEKKSKS GGRNNNGRIT TRHIGGGHKQ HYRLVDFRRN KDGIPAIVER VEYDPNRTA HIALLKYADG ERRYIIAPKG VAAGDQLISG IGAPIKAGNS MPLRNIPVGS TVHGIELKPG KGAQIARSAG A SAQLVARE ...String:
MAIVKCKPTS AGRRFVVKVV NQELHKGAPY APLLEKKSKS GGRNNNGRIT TRHIGGGHKQ HYRLVDFRRN KDGIPAIVER VEYDPNRTA HIALLKYADG ERRYIIAPKG VAAGDQLISG IGAPIKAGNS MPLRNIPVGS TVHGIELKPG KGAQIARSAG A SAQLVARE GAYVTLRLRS GEMRKVLAEC RATLGEVSNS EHSLRSLGKA GATRWRGVRP TVRGVAMNPV DHPHGGGEGR TS AGRHPVS PWGLQTKGKK TRSNKRTDNM IVRRRK

UniProtKB: Large ribosomal subunit protein uL2

+
Macromolecule #8: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 22.625695 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MTIGVVGRKC GMTRIFTEEG VSIPVTVIEV EPNRVTQFKT EETDGYRAVQ VTAGERRASR VTKAQAGHFA KANVAAGRGV WEFRLGEEQ YAAGDQITVD LFQAGQMVDV TGESKGKGFA GTIKRWNFRG QDNTHGNSVS HRVPGSIGQC QTPGRVFKGK K MSGHLGAE ...String:
MTIGVVGRKC GMTRIFTEEG VSIPVTVIEV EPNRVTQFKT EETDGYRAVQ VTAGERRASR VTKAQAGHFA KANVAAGRGV WEFRLGEEQ YAAGDQITVD LFQAGQMVDV TGESKGKGFA GTIKRWNFRG QDNTHGNSVS HRVPGSIGQC QTPGRVFKGK K MSGHLGAE RVTVQSLEIV RVDAERNLLL VKGAVPGATG GDVIVRPAAK ARG

UniProtKB: Large ribosomal subunit protein uL3

+
Macromolecule #10: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 21.673939 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MQLNVNGAQA IEVSERTFGG EFNETLVHQA VVAYMAGGRQ GSKAQKTRSE VSGGGKKPWR QKGTGRARAG TIRSPIWRGG GTTFAAKPR SHEQKLNKKM YRAALRSILA ELVRLDRLVV VADFAVDAPK TKGLVAKLDT LGLKDVLIVT DGVDENLYLA A RNLAHVDV ...String:
MQLNVNGAQA IEVSERTFGG EFNETLVHQA VVAYMAGGRQ GSKAQKTRSE VSGGGKKPWR QKGTGRARAG TIRSPIWRGG GTTFAAKPR SHEQKLNKKM YRAALRSILA ELVRLDRLVV VADFAVDAPK TKGLVAKLDT LGLKDVLIVT DGVDENLYLA A RNLAHVDV RDVQGSDPVS LIAYDKVLVT VSAVKKFEEL LG

UniProtKB: Large ribosomal subunit protein uL4

+
Macromolecule #11: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 20.42483 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MARLKEIYRK EIAPKLKEEL QLANVMEVPR VTKITLNMGL GEAVGDKKII ENAVADLEKI TGQKPVVTYA RKSIAGFKIR EGWPIGVKV TLRSDRMYEF LDRLLSISLP RVRDFRGLNA KSFDGRGNYS MGVKEQIIFP EIDYDKIDAL RGLDITLTTT A RTDDEGRA LLRAFKFPFR N

UniProtKB: Large ribosomal subunit protein uL5

+
Macromolecule #12: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 19.129145 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MSRVAKNPVK LPAGVEIKLA GQQLSIKGAK GALELKVHPS VEVIQDSGEL RFAARNGDQQ TRAMAGTTRA LVNNMVVGVS QGFERKLQL VGVGYKAQAK GQVLSLSLGF SHPVDYELPA GIVAETPSQT DILIKGIDKQ LVGQVAAEIR DFRPPEPYKG K GVRYADEV VRRKEAKKK

UniProtKB: Large ribosomal subunit protein uL6

+
Macromolecule #13: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 15.551678 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MEVILLEKVA NLGNLGDKVN IKGGYARNFL LPQGKATVAT AENVAAFEAR RAELEKAAAE KKAAAEARAA QLSELVVTLG AHAGDEGKL FGSIGTRDIA EAVSAAGYPL EKAEVRLPNG ALRNTGEFDV AVHLHTDVET TLKLIIVAE

UniProtKB: Large ribosomal subunit protein bL9

+
Macromolecule #14: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 16.058577 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MKTYTAKPET VQRDWFVVDA AGQTLGRLAT EIARRLRGKH KPEYTPHVDT GDYIVVINAE QVRVTGAKTT DKMYYHHSGF PGGIKSINF EKLIAKAPER VIETAVKGML PKNPLGRDMY RKLKVYKGAS HPHTAQQPQE LKI

UniProtKB: Large ribosomal subunit protein uL13

+
Macromolecule #15: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.43591 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MIQTQSMLDV ADNSGARRVM CIKVLGGSHR RYAGIGDIIK VTVKEAIPRG KVKKGQVMTA VVVRTKHGVR RTDGSIIRFD GNAAVLLNN KQEPIGTRIF GPVTRELRTE KFMKIVSLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #16: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 15.204488 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MQLNDLRSAP GARREKHRPG RGIGSGLGKT GGRGHKGLTS RSGGKVAPGF EGGQQPLHRR LPKFGFVSLK AMDRAEVRTS ELAKVEGDV VSLQTLKDAN LINQHVQRVK VMLSGEVGRA VTLKGIAATK GARAAIEAAG GKFED

UniProtKB: Large ribosomal subunit protein uL15

+
Macromolecule #17: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 7.934208 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MKADIHPTYE AIEATCSCGN VIKTRSTLCK PIHLDVCSEC HPFYTGKQKV LDTGGRIDRF KQRFGVFGAT K

UniProtKB: Large ribosomal subunit protein bL31

+
Macromolecule #18: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 15.434229 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MLQPKRTKFR KQMTGHNRGL AHRGSKVSFG EYALKATSRG RLTARQIESA RRALTRHVKR GGKIWIRVFP DKPVTKKPLE VRMGKGKGG VEYWVAQIQP GKVLYEIEGV SEELAREAFA LAAAKLPLAT SFVKRTVM

UniProtKB: Large ribosomal subunit protein uL16

+
Macromolecule #19: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 14.5339 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MRHRKSGRHL SRTSAHRKAM FQNMAVSLFE HELIKTTLPK AKELRRVAEP LITLAKEDSV ANRRLAFDRT RSKAAVGKLF NDLGKRYAN RPGGYLRILK CGFRAGDNAP MAYVELVDRP VGGEVVEAAE

UniProtKB: Large ribosomal subunit protein bL17

+
Macromolecule #20: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 12.687666 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MSVKKETRLR RARKARLKMR ELETVRLCVY RSSQHIYAQV IAADGGKVLA SASTLDKDLR EGATGNIDAA KKVGQLVAER AKAAGVTQV AFDRSGFKYH GRVKALADAA REGGLEF

UniProtKB: Large ribosomal subunit protein uL18

+
Macromolecule #21: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.055227 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MTNKIIQQIE AEQMNKEIPA FAPGDTVIVQ VKVKEGDRQR LQAFEGVVIA KRNRGLNSAF TVRKISNGVG VERTFQTYSP IVDSLSVKR RGDVRKAKLY YLRALSGKAA RIKEKLV

UniProtKB: Large ribosomal subunit protein bL19

+
Macromolecule #22: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.397972 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MARVKRGVIA RRRHKKILKL AKGYYGARSR VFRVAKQAVI KAGQYAYRDR RQRKRQFRAL WIARINAGAR QNGLSYSRLI AGLKKAAIE IDRKVLADLA VNEKAAFTAI VEKAKASLA

UniProtKB: Large ribosomal subunit protein bL20

+
Macromolecule #23: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 11.678621 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MYAVIVTGGK QHKVTEGEFL KVEKLDVATG EAIDFDRVLL VANGEDVKIG LPVVEGAKVT AEVVSHGRHD KVRIIKFRRR KHHMKRQGH RQWFTEIKIT GIQA

UniProtKB: Large ribosomal subunit protein bL21

+
Macromolecule #24: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 11.935996 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MEVAAKLSGA RISAQKARLV ADQIRGKKVG EALNLLAFSS KKAAEIMKKV LESAVANAEH NEGADVDDLK VSTVFVNEGR SLKRIMPRA KGRADRIVKR SCHITVKVAD K

UniProtKB: Large ribosomal subunit protein uL22

+
Macromolecule #25: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 10.969714 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MNQERVFKVL LGPHISEKAT GLADGKSQFV FKVATDATKL EIKKAVESLF SVKVQRVTTL NVKGKTKRTA RGLGKRNDWK KAYIALQPG QDLDFATSAE

UniProtKB: Large ribosomal subunit protein uL23

+
Macromolecule #26: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 11.494491 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MQKIRRDDEV IVIAGKDKGK RGKVLKVLAD DRLVVGGVNL IKRHTKPNPM LGQQGGIVEK EAPLHVSNVA IFNTETSKAD RVGFKVEDG KKIRVFKSTQ KPVQA

UniProtKB: Large ribosomal subunit protein uL24

+
Macromolecule #27: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 21.994242 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MVDFILNAQV RSDLGKGASR RLRRNAGLVP AVVYGGDKEP QSVTLELREI AKLLENEAAF SHVIALNVGG AKETVLIKAL QRHPAKGFV MHADFLRVVA DHKLTAHVPL HFINEEVAVG VKQAGGEISH TISEVEVSCL PKDLPEFIEV DMAKVELGQI V HLSDLKAP ...String:
MVDFILNAQV RSDLGKGASR RLRRNAGLVP AVVYGGDKEP QSVTLELREI AKLLENEAAF SHVIALNVGG AKETVLIKAL QRHPAKGFV MHADFLRVVA DHKLTAHVPL HFINEEVAVG VKQAGGEISH TISEVEVSCL PKDLPEFIEV DMAKVELGQI V HLSDLKAP KGVELVQLAH GNDLAVANIH ASRVVKEEGS EEGAAE

UniProtKB: Large ribosomal subunit protein bL25

+
Macromolecule #28: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 9.01045 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MAHKKAGGST RNGRDSESKR LGVKLFGGQA VKAGNILVRQ RGTKFHAGYG VGLGKDHTLF AKVDGVVKFE TKGAFGRKYV SIVAA

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #29: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 9.087633 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MSRVCQVTGK GPVTGNNISH AHNKTRRRFL PNLQHHRFWV ESEKRFVRLR VSAKGMRIID KRGIEAVLAD LRARGEKF

UniProtKB: Large ribosomal subunit protein bL28

+
Macromolecule #30: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 7.213352 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MKANELREKS VEQLNEQLLG LLRDQFNLRM QKATGQLGQS HLLSQVKRDI ARVKTVLNQQ AGK

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #31: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 6.489644 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MATVKVTLVK SLNGRLANHK ACVKGLGLRR INHTVEVQDT PENRGMINKA YYLLRVEG

UniProtKB: Large ribosomal subunit protein uL30

+
Macromolecule #33: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 27.376475 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MSQVNMRDML KAGVHFGHQT RYWNPKMGKF IFGARNKIHI INLEKTLPMF NEALTFVERL AAGKNKILFV GTKRSAGKIV REEAARCGM PYVDHRWLGG MLTNYKTIRQ SIKRLRDLET QSQDGTFDKL TKKEALMRSR DLEKLERSLG GIKDMGGLPD A LFVIDVDH ...String:
MSQVNMRDML KAGVHFGHQT RYWNPKMGKF IFGARNKIHI INLEKTLPMF NEALTFVERL AAGKNKILFV GTKRSAGKIV REEAARCGM PYVDHRWLGG MLTNYKTIRQ SIKRLRDLET QSQDGTFDKL TKKEALMRSR DLEKLERSLG GIKDMGGLPD A LFVIDVDH ERIAITEANK LGIPVIGVVD TNSSPEGVDY VIPGNDDAIR AVQLYLNSMA EAVIRGKQGA ATSADEFVEE AP AESAEG

UniProtKB: Small ribosomal subunit protein uS2

+
Macromolecule #34: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 25.887152 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MGQKVHPNGI RLGIVKEHTS VWYADRKNYA DYLFADLKVR EYLQDKLKSA SVSRIDIHRP AQTARITIHT ARPGIVIGKK GEDVEKLRQ DLTKQMGVPV HINIEEIRKP ELDAMLVAQS VAQQLERRVM FRRAMKRAVQ NAMRIGAKGI KIQVSGRLGG A EIARTEWY ...String:
MGQKVHPNGI RLGIVKEHTS VWYADRKNYA DYLFADLKVR EYLQDKLKSA SVSRIDIHRP AQTARITIHT ARPGIVIGKK GEDVEKLRQ DLTKQMGVPV HINIEEIRKP ELDAMLVAQS VAQQLERRVM FRRAMKRAVQ NAMRIGAKGI KIQVSGRLGG A EIARTEWY REGRVPLHTL RADIDYATYE AHTTYGVIGV KVWIFKGEVI GGRQEELKPV APAPRKKAAR

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #35: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 23.31867 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MARYIGPKCK LSRREGTDLF LKSGARALDS KCKAENVPGQ HGQRRGRLSD YGLQLREKQK VRRIYGVLER QFRGYYQEAS RRKGSTGEN LLQLLECRLD NVVYRMGFGS TRSESRQLVS HKAITVNGQT VNIPSYQVKA GDVVAVREKS KNQLRIAQAL E LCGQRGRV ...String:
MARYIGPKCK LSRREGTDLF LKSGARALDS KCKAENVPGQ HGQRRGRLSD YGLQLREKQK VRRIYGVLER QFRGYYQEAS RRKGSTGEN LLQLLECRLD NVVYRMGFGS TRSESRQLVS HKAITVNGQT VNIPSYQVKA GDVVAVREKS KNQLRIAQAL E LCGQRGRV EWVEVDLDKK AGTFKSAPAR SDLSADINEN LIVELYSK

UniProtKB: Small ribosomal subunit protein uS4

+
Macromolecule #36: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 17.650391 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MANNEQKRDE GYIEKLVQVN RVAKTVKGGR IFAFTALTVV GDGKGRVGFG RGKAREVPAA IQKAMEAARR NMIQVDLNGT TLQYPTKSA HGASKVYMQP ASEGTGIIAG GAMRAVLEVA GVQNVLAKCY GSTNPVNVVY ATFKGLKNMQ APEAVAAKRG K SVEEIL

UniProtKB: Small ribosomal subunit protein uS5

+
Macromolecule #37: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 16.189689 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MRHYEIVFLV HPDQSEQVGG MVERYTKAIE EDGGKIHRLE DWGRRQLAYA INNVHKAHYV LMNVECSAKA LAELEDNFRY NDAVIRNLV MRRDEAVTEQ SEMLKAEESR NERRERRERP NDNAEGADGD DNSDSDNADE

UniProtKB: Small ribosomal subunit protein bS6

+
Macromolecule #38: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 17.541514 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MPRRRVAAKR EVLADPKYGS QILAKFMNHV MESGKKAVAE RIVYGALDKV KERGKADPLE TFEKALDAIA PLVEVKSRRV GGATYQVPV EVRPSRRNAL AMRWLVDFAR KRGEKSMALR LAGELLDAAE GKGAAVKKRE DVHRMAEANK AFSHYRF

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #39: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 14.190609 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MSMQDPLADM LTRIRNAQMA EKTVVSMPSS KLKAAVAKVL KDEGYIADFQ ISSEVKPQLS IELKYFEGKP VIEEVKRISR PGLRQYKSV EQLPKVRGGL GVSIVSTNKG VMTDRAARAA GVGGEVLCTV F

UniProtKB: Small ribosomal subunit protein uS8

+
Macromolecule #40: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 14.643844 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MSATQNYGTG RRKTATARVF LRPGTGKISI NNRGLDQFFG RETARMVVRQ PLELTETVEK FDIFVTVVGG GVSGQAGAIR HGITRALIE YDETLRSSLR KAGYVTRDAR EVERKKVGLR KARKRPQYSK R

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #41: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 11.786605 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MQNQQIRIRL KAFDHRLIDQ STQEIVETAK RTGAQVRGPI PLPTRKERFT VLISPHVNKD ARDQYEIRTH KRVLDIVQPT DKTVDALMK LDLAAGVEVQ ISLG

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #42: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.654687 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MAKPAARPRK KVKKTVVDGI AHIHASFNNT IVTITDRQGN ALSWATSGGS GFRGSRKSTP FAAQVAAERA GQAALEYGLK NLDVNVKGP GPGRESAVRA LNACGYKIAS ITDVTPIPHN GCRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #43: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 43 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.830104 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MATINQLVRK PRKRMVDKSD VPALQNCPQR RGVCTRVYTT TPKKPNSALR KVCRVRLTNG FEVSSYIGGE GHNLQEHSVV LIRGGRVKD LPGVRYHTVR GSLDTSGVKD RKQGRSKYGA KRPK

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #44: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 44 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 13.292486 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MARIAGVNIP DNKHTVISLT YIYGVGRTTA QSICAATGVN PAAKIKDLSD EQIDQLRNEV AKITTEGDLR REINMNIKRL MDLGCYRGL RHRRGLPVRG QRTKTNARTR KGPRKPIRK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #45: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 45 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 11.591508 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MAKESMKNRE LKRQLTVAKY AKKRAELKAI IANPNSSAEE RWNAQVALQK QPRDASASRL RNRCRLTGRP HGFYRKFGLS RNKLREAAM RGDVPGLVKA SW

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #46: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 46 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 10.135661 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MALSVEEKAQ IVNEYKQAEG DTGSPEVQVA LLSANINKLQ DHFKANGKDH HSRRGLIRMV NQRRKLLDYL KGKDVSRYTA LIGRLGLRR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #47: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 47 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 9.219454 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MVTIRLARGG SKKRPFYHLT VTNSRNARDG RFVERIGFFN PVATGGEVRL SVDQERATYW LGQGAQPSER VAQLLKDAAK ANA

UniProtKB: Small ribosomal subunit protein bS16

+
Macromolecule #48: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 48 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 10.10682 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MAEAQKTVRT LTGRVVSDKM DKTVTVLIER RVKHPIYGKY VKRSTKLHAH DESNQCRIGD LVTIRETRPL AKTKAWTLVD IVERAVEV

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #49: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 49 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 8.892394 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MARFFRRRKF CRFTAEGVKE IDYKDLNTLK AYVSETGKIV PSRITGTKAK YQRQLATAIK RARYLALLPY TDSHGR

UniProtKB: Small ribosomal subunit protein bS18

+
Macromolecule #50: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 50 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 10.382331 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MPRSLKKGPF IDLHLLKKVE VAVEKNDRKP IKTWSRRSMI LPHMVGLTIA VHNGRQHVPV LVNEDMVGHK LGEFAATRTY RGHAADKKA KR

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #51: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 51 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 9.942673 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MANTPSAKKR AKQAEKRRSH NASLRSMVRT YIKNVVKAID AKDLEKAQAA FTAAVPVIDR MADKGIIHKN KAARHKSRLS GHIKALSTA AA

UniProtKB: Small ribosomal subunit protein bS20

+
Macromolecule #52: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 52 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 8.508979 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString:
MPAVKVKENE PFDVALRRFK RSCEKAGVLA EVRSREFYEK PTAERKRKAA AAVKRHAKKV QREQRRRERL Y

UniProtKB: Small ribosomal subunit protein bS21

+
Macromolecule #53: PHIKZ014

MacromoleculeName: PHIKZ014 / type: protein_or_peptide / ID: 53 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 43.374551 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa PAO1 (bacteria)
SequenceString: MKQYREPVTR LTKEKLEWVI SRRKERKAEQ PFGRAHFPAG TRAIFESCSL RYLDENERVY PGQRYETFEA TVLGVVANGH NSYVAILDM PCDLTESRNK AINVSWCRGI VSRGEGNFTW FKEESTEYDR NHGWNIREKH PTVRWAEGPR PTKVRSLTWA E EFDYNRAV ...String:
MKQYREPVTR LTKEKLEWVI SRRKERKAEQ PFGRAHFPAG TRAIFESCSL RYLDENERVY PGQRYETFEA TVLGVVANGH NSYVAILDM PCDLTESRNK AINVSWCRGI VSRGEGNFTW FKEESTEYDR NHGWNIREKH PTVRWAEGPR PTKVRSLTWA E EFDYNRAV DPVYIEINKH HSQYYITDMR SFVMFTLREH PAYANSFKDH LHKLDKLVMA LYSDPTIKAA EVKLSRYSVS WL ISKKKFH KVLQRLLPFY KTSRRKAQEE DDKAISEMYE AELDRDLSEQ YGESDDTSDE SSYSWNDSTP LDDDDLNVFD MYD DSACSR EISDDVQPKT IGELLREAME NPEEEKSKLV IGSMETLSKA VIIK

UniProtKB: PHIKZ014

+
Macromolecule #5: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 935.990438 KDa
SequenceString: GUCAAGUGAA GAAGCGCAUA CGGUGGAUGC CUUGGCAGUC AGAGGCGAUG AAAGACGUGG UAGCCUGCGA AAAGCUUCGG GGAGUCGGC AAACAGACUU UGAUCCGGAG AUCUCUGAAU GGGGGAACCC ACCUAGGAUA ACCUAGGUAU CUUGUACUGA A UCCAUAGG ...String:
GUCAAGUGAA GAAGCGCAUA CGGUGGAUGC CUUGGCAGUC AGAGGCGAUG AAAGACGUGG UAGCCUGCGA AAAGCUUCGG GGAGUCGGC AAACAGACUU UGAUCCGGAG AUCUCUGAAU GGGGGAACCC ACCUAGGAUA ACCUAGGUAU CUUGUACUGA A UCCAUAGG UGCAAGAGGC GAACCAGGGG AACUGAAACA UCUAAGUACC CUGAGGAAAA GAAAUCAACC GAGAUUCCCU UA GUAGUGG CGAGCGAACG GGGAUUAGCC CUUAAGCUUC AUUGAUUUUA GCGGAACGCU CUGGAAAGUG CGGCCAUAGU GGG UGAUAG CCCCGUACGC GAAAGGAUCU UUGAAGUGAA AUCAAGUAGG ACGGAGCACG AGAAACUUUG UCUGAACAUG GGGG GACCA UCCUCCAAGG CUAAAUACUA CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAAGAACC CCGGA GAGG GGAGUGAAAU AGAACCUGAA ACCGUAUGCG UACAAGCAGU GGGAGCCUAC UUGUUAGGUG ACUGCGUACC UUUUGU AUA AUGGGUCAGC GACUUAUAUU CAGUGGCAAG CUUAACCGUA UAGGGUAGGC GUAGCGAAAG CGAGUCUUAA UAGGGCG UU UAGUCGCUGG GUAUAGACCC GAAACCGGGC GAUCUAUCCA UGAGCAGGUU GAAGGUUAGG UAACACUGAC UGGAGGAC C GAACCCACUC CCGUUGAAAA GGUAGGGGAU GACUUGUGGA UCGGAGUGAA AGGCUAAUCA AGCUCGGAGA UAGCUGGUU CUCCUCGAAA GCUAUUUAGG UAGCGCCUCA UGUAUCACUC UGGGGGGUAG AGCACUGUUU CGGCUAGGGG GUCAUCCCGA CUUACCAAA CCGAUGCAAA CUCCGAAUAC CCAGAAGUGC CGAGCAUGGG AGACACACGG CGGGUGCUAA CGUCCGUCGU G AAAAGGGA AACAACCCAG ACCGCCAGCU AAGGUCCCAA AGUUGUGGUU AAGUGGUAAA CGAUGUGGGA AGGCUUAGAC AG CUAGGAG GUUGGCUUAG AAGCAGCCAC CCUUUAAAGA AAGCGUAAUA GCUCACUAGU CGAGUCGGCC UGCGCGGAAG AUG UAACGG GGCUCAAACC ACACACCGAA GCUGCGGGUG UCACGUAAGU GACGCGGUAG AGGAGCGUUC UGUAAGCCUG UGAA GGUGA GUUGAGAAGC UUGCUGGAGG UAUCAGAAGU GCGAAUGCUG ACAUGAGUAA CGACAAUGGG UGUGAAAAAC ACCCA CGCC GAAAGACCAA GGGUUCCUGC GCAACGUUAA UCGACGCAGG GUUAGUCGGU UCCUAAGGCG AGGCUGAAAA GCGUAG UCG AUGGGAAACA GGUUAAUAUU CCUGUACUUC UGGUUACUGC GAUGGAGGGA CGGAGAAGGC UAGGCCAGCU UGGCGUU GG UUGUCCAAGU UUAAGGUGGU AGGCUGAAAU CUUAGGUAAA UCCGGGGUUU CAAGGCCGAG AGCUGAUGAC GAGUCGUC U UUUAGAUGAC GAAGUGGUUG AUGCCAUGCU UCCAAGAAAA GCUUCUAAGC UUCAGGUAAC CAGGAACCGU ACCCCAAAC CGACACAGGU GGUCGGGUAG AGAAUACCAA GGCGCUUGAG AGAACUCGGG UGAAGGAACU AGGCAAAAUG GCACCGUAAC UUCGGGAGA AGGUGCGCCG GCUAGGGUGA AGGAUUUACU CCGUAAGCUC UGGCUGGUCG AAGAUACCAG GCCGCUGCGA C UGUUUAUU AAAAACACAG CACUCUGCAA ACACGAAAGU GGACGUAUAG GGUGUGACGC CUGCCCGGUG CCGGAAGGUU AA UUGAUGG GGUUAGCGCA AGCGAAGCUC UUGAUCGAAG CCCCGGUAAA CGGCGGCCGU AACUAUAACG GUCCUAAGGU AGC GAAAUU CCUUGUCGGG UAAGUUCCGA CCUGCACGAA UGGCGUAACG AUGGCGGCGC UGUCUCCACC CGAGACUCAG UGAA AUUGA AAUCGCUGUG AAGAUGCAGU GUAUCCGCGG CUAGACGGAA AGACCCCGUG AACCUUUACU GUAGCUUUGC ACUGG ACUU UGAGCCUGCU UGUGUAGGAU AGGUGGGAGG CUUUGAAGCG UGGACGCCAG UUCGCGUGGA GCCAUCCUUG AAAUAC CAC CCUGGCAUGC UUGAGGUUCU AACUCUGGUC CGUAAUCCGG AUCGAGGACA GUGUAUGGUG GGCAGUUUGA CUGGGGC GG UCUCCUCCUA AAGAGUAACG GAGGAGUACG AAGGUGCGCU CAGACCGGUC GGAAAUCGGU CGCAGAGUAU AAAGGCAA A AGCGCGCUUG ACUGCGAGAC AGACACGUCG AGCAGGUACG AAAGUAGGUC UUAGUGAUCC GGUGGUUCUG UAUGGAAGG GCCAUCGCUC AACGGAUAAA AGGUACUCCG GGGAUAACAG GCUGAUACCG CCCAAGAGUU CAUAUCGACG GCGGUGUUUG GCACCUCGA UGUCGGCUCA UCACAUCCUG GGGCUGAAGC CGGUCCCAAG GGUAUGGCUG UUCGCCAUUU AAAGUGGUAC G CGAGCUGG GUUUAGAACG UCGUGAGACA GUUCGGUCCC UAUCUGCCGU GGACGUUUGA GAUUUGAGAG GGGCUGCUCC UA GUACGAG AGGACCGGAG UGGACGAACC UCUGGUGUUC CGGUUGUCAC GCCAGUGGCA UUGCCGGGUA GCUAUGUUCG GAA AAGAUA ACCGCUGAAA GCAUCUAAGC GGGAAACUUG CCUCAAGAUG AGAUCUCACU GGGAACUUGA UUCCCCUGAA GGGC CGUCG AAGACUACGA CGUUGAUAGG CUGGGUGUGU AAGCGUUGUG AGGCGUUGAG CUAACCAGUA CUAAUGGCCC GUGAG GCUU GACC

+
Macromolecule #6: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 38.596898 KDa
SequenceString:
UGCUUGACGA UCAUAGAGCG UUGGAACCAC CUGAUCCCUU CCCGAACUCA GAAGUGAAAC GACGCAUCGC CGAUGGUAGU GUGGGGUCU CCCCAUGUGA GAGUAGGUCA UCGUCAAGCU C

+
Macromolecule #9: tRNA

MacromoleculeName: tRNA / type: rna / ID: 9 / Details: modified bases were mutated to canonical ones. / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 24.485539 KDa
SequenceString:
GCCCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUGAAAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGG GCACCA

+
Macromolecule #32: 16S rRNA

MacromoleculeName: 16S rRNA / type: rna / ID: 32 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 494.643906 KDa
SequenceString: AACUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAGCGGAU AAAGGGAGCU UGCUCCUGG AUUCAGCGGC GGACGGGUGA GUAAUGCCUA GGAAUCUGCC UGGUAGUGGG GGAUAACGUC CGGAAACGGG C GCUAAUAC ...String:
AACUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAGCGGAU AAAGGGAGCU UGCUCCUGG AUUCAGCGGC GGACGGGUGA GUAAUGCCUA GGAAUCUGCC UGGUAGUGGG GGAUAACGUC CGGAAACGGG C GCUAAUAC CGCAUACGUC CUGAGGGAGA AAGUGGGGGA UCUUCGGACC UCACGCUAUC AGAUGAGCCU AGGUCGGAUU AG CUAGUUG GUGGGGUAAA GGCCUACCAA GGCGACGAUC CGUAACUGGU CUGAGAGGAU GAUCAGUCAC ACUGGAACUG AGA CACGGU CCAGACUCCU ACGGGAGGCA GCAGUGGGGA AUAUUGGACA AUGGGCGAAA GCCUGAUCCA GCCAUGCCGC GUGU GUGAA GAAGGUCUUC GGAUUGUAAA GCACUUUAAG UUGGGAGGAA GGGCAGUAAG UUAAUACCUU GCUGUUUUGA CGUUA CCAA CAGAAUAAGC ACCGGCUAAC UUCGUGCCAG CAGCCGCGGU AAUACGAAGG GUGCAAGCGU UAAUCGGAAU UACUGG GCG UAAAGCGCGC GUAGGUGGUU CAGCAAGUUG GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCCAA AACUACU GA GCUAGAGUAC GGUAGAGGGU GGUGGAAUUU CCUGUGUAGC GGUGAAAUGC GUAGAUAUAG GAAGGAACAC CAGUGGCG A AGGCGACCAC CUGGACUGAU ACUGACACUG AGGUGCGAAA GCGUGGGGAG CAAACAGGAU UAGAUACCCU GGUAGUCCA CGCCGUAAAC GAUGUCGACU AGCCGUUGGG AUCCUUGAGA UCUUAGUGGC GCAGCUAACG CGAUAAGUCG ACCGCCUGGG GAGUACGGC CGCAAGGUUA AAACUCAAAU GAAUUGACGG GGGCCCGCAC AAGCGGUGGA GCAUGUGGUU UAAUUCGAAG C AACGCGAA GAACCUUACC UGGCCUUGAC AUGCUGAGAA CUUUCCAGAG AUGGAUUGGU GCCUUCGGGA ACUCAGACAC AG GUGCUGC AUGGCUGUCG UCAGCUCGUG UCGUGAGAUG UUGGGUUAAG UCCCGUAACG AGCGCAACCC UUGUCCUUAG UUA CCAGCA CCUCGGGUGG GCACUCUAAG GAGACUGCCG GUGACAAACC GGAGGAAGGU GGGGAUGACG UCAAGUCAUC AUGG CCCUU ACGGCCAGGG CUACACACGU GCUACAAUGG UCGGUACAAA GGGUUGCCAA GCCGCGAGGU GGAGCUAAUC CCAUA AAAC CGAUCGUAGU CCGGAUCGCA GUCUGCAACU CGACUGCGUG AAGUCGGAAU CGCUAGUAAU CGUGAAUCAG AAUGUC ACG GUGAAUACGU UCCCGGGCCU UGUACACACC GCCCGUCACA CCAUGGGAGU GGGUUGCUCC AGAAGUAGCU AGUCUAA CC GCAAGGGGGA CGGUUACCAC GGAGUGAUUC AUGACUGGGG UGAAGUCGUA ACAAGGUAGC CGUAGGGGAA CCUGCGGC U GGAUC

+
Macromolecule #54: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 54 / Number of copies: 171 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Details: 20 mM HEPES/KOH pH 7.5, 150 mM KCl, 16 mM MgCl2, 1 mM DTT, 0.1% TritonX100
GridModel: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8431 / Average exposure time: 5.16 sec. / Average electron dose: 88.28 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1852441
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6spg

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 169672
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8cd1:
70S-PHIKZ014

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more