[English] 日本語
Yorodumi
- EMDB-0139: Structure of a hibernating 100S ribosome reveals an inactive conf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0139
TitleStructure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome
Map data
Sample
  • Complex: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1
    • Protein or peptide: x 52 types
    • RNA: x 4 types
Function / homology
Function and homology information


negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / primary metabolic process / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding ...negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / primary metabolic process / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / ribosomal small subunit binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / negative regulation of translational initiation / four-way junction DNA binding / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / transcription elongation factor complex / positive regulation of RNA splicing / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / DNA endonuclease activity / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / : / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / regulation of translation / ribosome biogenesis / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / single-stranded RNA binding / molecular adaptor activity / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosome modulation factor / Ribosome modulation factor domain superfamily / Ribosome modulation factor / Ribosomal protein S1 / Ribosomal protein S1-like / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / S1 domain profile. / Ribosomal protein S21, conserved site ...Ribosome modulation factor / Ribosome modulation factor domain superfamily / Ribosome modulation factor / Ribosomal protein S1 / Ribosomal protein S1-like / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / S1 domain profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / 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 L33, conserved site / Ribosomal protein L33 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 L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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 L14P, bacterial-type / Ribosomal protein S4, 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 L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type
Similarity search - Domain/homology
Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 ...Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Ribosome modulation factor / Ribosome hibernation promoting factor / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS1 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsBeckert B / Turk M / Czech A / Berninghausen O / Beckmann R / Ignatova Z / Plitzko J / Wilson DN
CitationJournal: Nat Microbiol / Year: 2018
Title: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.
Authors: Bertrand Beckert / Martin Turk / Andreas Czech / Otto Berninghausen / Roland Beckmann / Zoya Ignatova / Jürgen M Plitzko / Daniel N Wilson /
Abstract: To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S ...To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF). Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria, and reveals a unique role for bS1 in translation regulation.
History
DepositionJul 24, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseSep 5, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.075
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.075
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6h58
  • Surface level: 0.075
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0139.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy AUTHOR: 0.075 / Movie #1: 0.075
Minimum - Maximum-0.09665876 - 0.31201142
Average (Standard dev.)0.0033455554 (±0.019324372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions228228228
Spacing228228228
CellA=B=C: 615.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z228228228
origin x/y/z0.0000.0000.000
length x/y/z615.600615.600615.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS228228228
D min/max/mean-0.0970.3120.003

-
Supplemental data

-
Additional map: #1

Fileemd_0139_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: #2

Fileemd_0139_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : Structure of a hibernating 100S ribosome reveals an inactive conf...

EntireName: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1
Components
  • Complex: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
    • Protein or peptide: 50S ribosomal protein L31
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • 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 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: 50S ribosomal protein L22
    • 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 ribosomal RNA
    • 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: Ribosome modulation factor
    • Protein or peptide: Ribosome hibernation promoting factor
    • Protein or peptide: 30S ribosomal protein S1
    • RNA: tRNA Mixture

+
Supramolecule #1: Structure of a hibernating 100S ribosome reveals an inactive conf...

SupramoleculeName: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#56
Details: single particle cryo-electron microscopy structures of hibernating 100S particles isolated from stationary phase E. coli cells
Source (natural)Organism: Escherichia coli BW25113 (bacteria)

+
Macromolecule #1: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 6.332249 KDa
SequenceString:
AVQQNKPTRS KRGMRRSHDA LTAVTSLSVD KTSGEKHLRH HITADGYYRG RKVIAK

+
Macromolecule #2: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 5.814842 KDa
SequenceString:
GIREKIKLVS SAGTGHFYTT TKNKRTKPEK LELKKFDPVV RQHVIYKEAK

+
Macromolecule #3: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 5.397463 KDa
SequenceString:
MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

+
Macromolecule #4: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 7.181835 KDa
SequenceString:
PKIKTVRGAA KRFKKTGKGG FKHKHANLRH ILTKKATKRK RHLRPKAMVS KGDLGLVIAC LPYA

+
Macromolecule #5: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 4.37739 KDa
SequenceString:
MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG

+
Macromolecule #6: 50S ribosomal protein L31

MacromoleculeName: 50S ribosomal protein L31 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 7.516693 KDa
SequenceString:
MKKDIHPKYE EITASCSCGN VMKIRSTVGH DLNLDVCSKC HPFFTGKQRD VATGGRVDRF NKRFNI

+
Macromolecule #9: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 29.663244 KDa
SequenceString: AVVKCKPTSP GRRHVVKVVN PELHKGKPFA PLLEKNSKSG GRNNNGRITT RHIGGGHKQA YRIVDFKRNK DGIPAVVERL EYDPNRSAN IALVLYKDGE RRYILAPKGL KAGDQIQSGV DAAIKPGNTL PMRNIPVGST VHNVEMKPGK GGQLARSAGT Y VQIVARDG ...String:
AVVKCKPTSP GRRHVVKVVN PELHKGKPFA PLLEKNSKSG GRNNNGRITT RHIGGGHKQA YRIVDFKRNK DGIPAVVERL EYDPNRSAN IALVLYKDGE RRYILAPKGL KAGDQIQSGV DAAIKPGNTL PMRNIPVGST VHNVEMKPGK GGQLARSAGT Y VQIVARDG AYVTLRLRSG EMRKVEADCR ATLGEVGNAE HMLRVLGKAG AARWRGVRPT VRGTAMNPVD HPHGGGEGRN FG KHPVTPW GVQTKGKKTR SNKRTDKFIV RRRS

+
Macromolecule #10: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 22.277535 KDa
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN QTPGKVFKGK K MAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

+
Macromolecule #11: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 22.121566 KDa
SequenceString: MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD ...String:
MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW RQKGTGRARS GSIKSPIWRS GGVTFAARP QDHSQKVNKK MYRGALKSIL SELVRQDRLI VVEKFSVEAP KTKLLAQKLK DMALEDVLII TGELDENLFL A ARNLHKVD VRDATGIDPV SLIAFDKVVM TADAVKQVEE MLA

+
Macromolecule #12: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 20.073234 KDa
SequenceString:
AKLHDYYKDE VVKKLMTEFN YNSVMQVPRV EKITLNMGVG EAIADKKLLD NAAADLAAIS GQKPLITKAR KSVAGFKIRQ GYPIGCKVT LRGERMWEFF ERLITIAVPR IRDFRGLSAK SFDGRGNYSM GVREQIIFPE IDYDKVDRVR GLDITITTTA K SDEEGRAL LAAFDFPFR

+
Macromolecule #13: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 18.801598 KDa
SequenceString:
SRVAKAPVVV PAGVDVKING QVITIKGKNG ELTRTLNDAV EVKHADNTLT FGPRDGYADG WAQAGTARAL LNSMVIGVTE GFTKKLQLV GVGYRAAVKG NVINLSLGFS HPVDHQLPAG ITAECPTQTE IVLKGADKQV IGQVAADLRA YRRPEPYKGK G VRYADEVV RTKEAKKK

+
Macromolecule #14: 50S ribosomal protein L9

MacromoleculeName: 50S ribosomal protein L9 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 15.78902 KDa
SequenceString:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE

+
Macromolecule #15: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 16.050606 KDa
SequenceString:
MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

+
Macromolecule #16: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 13.45191 KDa
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEV

+
Macromolecule #17: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 14.877273 KDa
SequenceString:
RLNTLSPAEG SKKAGKRLGR GIGSGLGKTG GRGHKGQKSR SGGGVRRGFE GGQMPLYRRL PKFGFTSRKA AITAEIRLSD LAKVEGGVV DLNTLKAANI IGIQIEFAKV ILAGEVTTPV TVRGLRVTKG ARAAIEAAGG KIEE

+
Macromolecule #18: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 15.312269 KDa
SequenceString:
MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV RMGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM

+
Macromolecule #19: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 13.721938 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS E

+
Macromolecule #20: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 12.663471 KDa
SequenceString:
DKKSARIRRA TRARRKLQEL GATRLVVHRT PRHIYAQVIA PNGSEVLVAA STVEKAIAEQ LKYTGNKDAA AAVGKAVAER ALEKGIKDV SFDRSGFQYH GRVQALADAA REAGLQF

+
Macromolecule #21: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 13.028082 KDa
SequenceString:
SNIIKQLEQE QMKQDVPSFR PGDTVEVKVW VVEGSKKRLQ AFEGVVIAIR NRGLHSAFTV RKISNGEGVE RVFQTHSPVV DSISVKRRG AVRKAKLYYL RERTGKAARI KERLN

+
Macromolecule #22: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 13.396828 KDa
SequenceString:
ARVKRGVIAR ARHKKILKQA KGYYGARSRV YRVAFQAVIK AGQYAYRDRR QRKRQFRQLW IARINAAARQ NGISYSKFIN GLKKASVEI DRKILADIAV FDKVAFTALV EKAKAALA

+
Macromolecule #23: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 11.586374 KDa
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

+
Macromolecule #24: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 12.253359 KDa
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

+
Macromolecule #25: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 10.546472 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNL

+
Macromolecule #26: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 11.078874 KDa
SequenceString:
AAKIRRDDEV IVLTGKDKGK RGKVKNVLSS GKVIVEGINL VKKHQKPVPA LNQPGGIVEK EAAIQVSNVA IFNAATGKAD RVGFRFEDG KKVRFFKSNS ETI

+
Macromolecule #27: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 10.713465 KDa
SequenceString:
MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA

+
Macromolecule #28: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 8.174394 KDa
SequenceString:
RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

+
Macromolecule #29: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 29 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 8.896354 KDa
SequenceString:
SRVCQVTGKR PVTGNNRSHA LNATKRRFLP NLHSHRFWVE SEKRFVTLRV SAKGMRVIDK KGIDTVLAEL RARGEKY

+
Macromolecule #30: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 30 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 7.286464 KDa
SequenceString:
MKAKELREKS VEELNTELLN LLREQFNLRM QAASGQLQQS HLLKQVRRDV ARVKTLLNEK AGA

+
Macromolecule #31: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 31 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 6.423625 KDa
SequenceString:
AKTIKITQTR SAIGRLPKHK ATLLGLGLRR IGHTVEREDT PAIRGMINAV SFMVKVEE

+
Macromolecule #33: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 33 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 25.096799 KDa
SequenceString: MLKAGVHFGH QTRYWNPKMK PFIFGARNKV HIINLEKTVP MFNEALAELN KIASRKGKIL FVGTKRAASE AVKDAALSCD QFFVNHRWL GGMLTNWKTV RQSIKRLKDL ETQSQDGTFD KLTKKEALMR TRELEKLENS LGGIKDMGGL PDALFVIDAD H EHIAIKEA ...String:
MLKAGVHFGH QTRYWNPKMK PFIFGARNKV HIINLEKTVP MFNEALAELN KIASRKGKIL FVGTKRAASE AVKDAALSCD QFFVNHRWL GGMLTNWKTV RQSIKRLKDL ETQSQDGTFD KLTKKEALMR TRELEKLENS LGGIKDMGGL PDALFVIDAD H EHIAIKEA NNLGIPVFAI VDTNSDPDGV DFVIPGNDDA IRAVTLYLGA VAATVREGRS QDLASQAE

+
Macromolecule #34: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 34 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 23.078785 KDa
SequenceString: GQKVHPNGIR LGIVKPWNST WFANTKEFAD NLDSDFKVRQ YLTKELAKAS VSRIVIERPA KSIRVTIHTA RPGIVIGKKG EDVEKLRKV VADIAGVPAQ INIAEVRKPE LDAKLVADSI TSQLERRVMF RRAMKRAVQN AMRLGAKGIK VEVSGRLGGA E IARTEWYR ...String:
GQKVHPNGIR LGIVKPWNST WFANTKEFAD NLDSDFKVRQ YLTKELAKAS VSRIVIERPA KSIRVTIHTA RPGIVIGKKG EDVEKLRKV VADIAGVPAQ INIAEVRKPE LDAKLVADSI TSQLERRVMF RRAMKRAVQN AMRLGAKGIK VEVSGRLGGA E IARTEWYR EGRVPLHTLR ADIDYNTSEA HTTYGVIGVK VWIFKGEI

+
Macromolecule #35: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 35 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 23.383002 KDa
SequenceString: ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT ...String:
ARYLGPKLKL SRREGTDLFL KSGVRAIDTK CKIEQAPGQH GARKPRLSDY GVQLREKQKV RRIYGVLERQ FRNYYKEAAR LKGNTGENL LALLEGRLDN VVYRMGFGAT RAEARQLVSH KAIMVNGRVV NIASYQVSPN DVVSIREKAK KQSRVKAALE L AEQREKPT WLEVDAGKME GTFKRKPERS DLSADINEHL IVELYSK

+
Macromolecule #36: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 36 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 16.532088 KDa
SequenceString:
ELQEKLIAVN RVSKTVKGGR IFSFTALTVV GDGNGRVGFG YGKAREVPAA IQKAMEKARR NMINVALNNG TLQHPVKGVH TGSRVFMQP ASEGTGIIAG GAMRAVLEVA GVHNVLAKAY GSTNPINVVR ATIDGLENMN SPEMVAAKRG KSVEEILG

+
Macromolecule #37: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 37 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 11.669371 KDa
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA S

+
Macromolecule #38: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 38 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 18.048879 KDa
SequenceString:
PRRRVIGQRK ILPDPKFGSE LLAKFVNILM VDGKKSTAES IVYSALETLA QRSGKSELEA FEVALENVRP TVEVKSRRVG GSTYQVPVE VRPVRRNALA MRWIVEAARK RGDKSMALRL ANELSDAAEN KGTAVKKRED VHRMAEANKA FAHYAWLSLR S A

+
Macromolecule #39: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 39 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 14.015361 KDa
SequenceString:
SMQDPIADML TRIRNGQAAN KAAVTMPSSK LKVAIANVLK EEGFIEDFKV EGDTKPELEL TLKYFQGKAV VESIQRVSRP GLRIYKRKD ELPKVMAGLG IAVVSTSKGV MTDRAARQAG LGGEIICYVA

+
Macromolecule #40: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 40 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 14.554882 KDa
SequenceString:
NQYYGTGRRK SSAARVFIKP GNGKIVINQR SLEQYFGRET ARMVVRQPLE LVDMVEKLDL YITVKGGGIS GQAGAIRHGI TRALMEYDE SLRSELRKAG FVTRDARQVE RKKVGLRKAR RRPQFSKR

+
Macromolecule #41: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 41 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 11.196988 KDa
SequenceString:
RIRIRLKAFD HRLIDQATAE IVETAKRTGA QVRGPIPLPT RKERFTVLIS PHVNKDARDQ YEIRTHLRLV DIVEPTEKTV DALMRLDLA AGVDVQISL

+
Macromolecule #42: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 42 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 12.388068 KDa
SequenceString:
RKQVSDGVAH IHASFNNTIV TITDRQGNAL GWATAGGSGF RGSRKSTPFA AQVAAERCAD AVKEYGIKNL EVMVKGPGPG RESTIRALN AAGFRITNIT DVTPIPHNGC RPPKKRR

+
Macromolecule #43: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 43 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 13.636961 KDa
SequenceString:
ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVKDL PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

+
Macromolecule #44: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 44 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 12.625753 KDa
SequenceString:
ARIAGINIPD HKHAVIALTS IYGVGKTRSK AILAAAGIAE DVKISELSEG QIDTLRDEVA KFVVEGDLRR EISMSIKRLM DLGCYRGLR HRRGLPVRGQ RTKTNARTRK GPRKP

+
Macromolecule #45: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 45 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 11.546442 KDa
SequenceString:
AKQSMKAREV KRVALADKYF AKRAELKAII SDVNAASDED RWNAVLKLQT LPRDSSPSRQ RNRCRQTGRP HGFLRKFGLS RIKVREAAM RGEIPGLKKA SW

+
Macromolecule #46: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 46 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 10.159621 KDa
SequenceString:
SLSTEATAKI VSEFGRDAND TGSTEVQVAL LTAQINHLQG HFAEHKKDHH SRRGLLRMVS QRRKLLDYLK RKDVARYTQL IERLGLRR

+
Macromolecule #47: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 47 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 9.207572 KDa
SequenceString:
MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

+
Macromolecule #48: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 48 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 9.263946 KDa
SequenceString:
KIRTLQGRVV SDKMEKSIVV AIERFVKHPI YGKFIKRTTK LHVHDENNEC GIGDVVEIRE CRPLSKTKSW TLVRVVEKAV

+
Macromolecule #49: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 49 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 7.606768 KDa
SequenceString:
FCRFTAEGVQ EIDYKDIATL KNYITESGKI VPSRITGTRA KYQRQLARAI KRARYLSLLP YTDRH

+
Macromolecule #50: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 50 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 9.057626 KDa
SequenceString:
RSLKKGPFID LHLLKKVEKA VESGDKKPLR TWSRRSTIFP NMIGLTIAVH NGRQHVPVFV TDEMVGHKLG EFAPTRTYR

+
Macromolecule #51: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 51 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 9.50619 KDa
SequenceString:
NIKSAKKRAI QSEKARKHNA SRRSMMRTFI KKVYAAIEAG DKAAAQKAFN EMQPIVDRQA AKGLIHKNKA ARHKANLTAQ INKLA

+
Macromolecule #52: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 52 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 7.763073 KDa
SequenceString:
IKVRENEPFD VALRRFKRSC EKAGVLAEVR RREFYEKPTT ERKRAKASAV KRHAKKLARE NARRT

+
Macromolecule #53: Ribosome modulation factor

MacromoleculeName: Ribosome modulation factor / type: protein_or_peptide / ID: 53 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 6.520523 KDa
SequenceString:
MKRQKRDRLE RAHQRGYQAG IAGRSKEMCP YQTLNQRSQW LGGWREAMAD RVVMA

+
Macromolecule #54: Ribosome hibernation promoting factor

MacromoleculeName: Ribosome hibernation promoting factor / type: protein_or_peptide / ID: 54 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 10.76823 KDa
SequenceString:
MQLNITGNNV EITEALREFV TAKFAKLEQY FDRINQVYVV LKVEKVTHTS DATLHVDGGE LHASAEGQDM YAAIDGLIDK LARQLTKHK DKLKQH

+
Macromolecule #55: 30S ribosomal protein S1

MacromoleculeName: 30S ribosomal protein S1 / type: protein_or_peptide / ID: 55 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 61.238887 KDa
SequenceString: MTESFAQLFE ESLKEIETRP GSIVRGVVVA IDKDVVLVDA GLKSESAIPA EQFKNAQGEL EIQVGDEVDV ALDAVEDGFG ETLLSREKA KRHEAWITLE KAYEDAETVT GVINGKVKGG FTVELNGIRA FLPGSLVDVR PVRDTLHLEG KELEFKVIKL D QKRNNVVV ...String:
MTESFAQLFE ESLKEIETRP GSIVRGVVVA IDKDVVLVDA GLKSESAIPA EQFKNAQGEL EIQVGDEVDV ALDAVEDGFG ETLLSREKA KRHEAWITLE KAYEDAETVT GVINGKVKGG FTVELNGIRA FLPGSLVDVR PVRDTLHLEG KELEFKVIKL D QKRNNVVV SRRAVIESEN SAERDQLLEN LQEGMEVKGI VKNLTDYGAF VDLGGVDGLL HITDMAWKRV KHPSEIVNVG DE ITVKVLK FDRERTRVSL GLKQLGEDPW VAIAKRYPEG TKLTGRVTNL TDYGCFVEIE EGVEGLVHVS EMDWTNKNIH PSK VVNVGD VVEVMVLDID EERRRISLGL KQCKANPWQQ FAETHNKGDR VEGKIKSITD FGIFIGLDGG IDGLVHLSDI SWNV AGEEA VREYKKGDEI AAVVLQVDAE RERISLGVKQ LAEDPFNNWV ALNKKGAIVT GKVTAVDAKG ATVELADGVE GYLRA SEAS RDRVEDATLV LSVGDEVEAK FTGVDRKNRA ISLSVRAKDE ADEKDAIATV NKQEDANFSN NAMAEAFKAA KGE

+
Macromolecule #7: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 7 / Number of copies: 2
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 941.30525 KDa
SequenceString: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG ...String:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGA UAUGAACCGU UAUAACCGGC GAUUUCCGAA UGGGGAAACC CAGUGUGUUU CGACACACUA UCAUUAACUG A AUCCAUAG GUUAAUGAGG CGAACCGGGG GAACUGAAAC AUCUAAGUAC CCCGAGGAAA AGAAAUCAAC CGAGAUUCCC CC AGUAGCG GCGAGCGAAC GGGGAGCAGC CCAGAGCCUG AAUCAGUGUG UGUGUUAGUG GAAGCGUCUG GAAAGGCGCG CGA UACAGG GUGACAGCCC CGUACACAAA AAUGCACAUG CUGUGAGCUC GAUGAGUAGG GCGGGACACG UGGUAUCCUG UCUG AAUAU GGGGGGACCA UCCUCCAAGG CUAAAUACUC CUGACUGACC GAUAGUGAAC CAGUACCGUG AGGGAAAGGC GAAAA GAAC CCCGGCGAGG GGAGUGAAAA AGAACCUGAA ACCGUGUACG UACAAGCAGU GGGAGCACGC UUAGGCGUGU GACUGC GUA CCUUUUGUAU AAUGGGUCAG CGACUUAUAU UCUGUAGCAA GGUUAACCGA AUAGGGGAGC CGAAGGGAAA CCGAGUC UU AACUGGGCGU UAAGUUGCAG GGUAUAGACC CGAAACCCGG UGAUCUAGCC AUGGGCAGGU UGAAGGUUGG GUAACACU A ACUGGAGGAC CGAACCGACU AAUGUCGAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCAAUC AAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAUCC CGACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCACGG GAGACACACG GCGGGUGCUA A CGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGUCAUGGU UAAGUGGGAA ACGAUGUGGG AA GGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGCGUAAU AGCUCACUGG UCGAGUCGGC CUG CGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGCUUAU GCGUUGUUGG GUAGGGGAGC GUUC UGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCGAAU GCUGACAUAA GUAACGAUAA AGCGG GUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGGGG CAGGGUGAGU CGACCCCUAA GGCGAG GCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUUA CUGCGAAGGG GGGACGGAGA AGGCUAU GU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGGA AAAUCAAGGC UGAGGCGU G AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA AGCCUCUAAG CAUCAGGUAA CAUCAAAUC GUACCCCAAA CCGACACAGG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCCU CGCGGAUGGA GCUGAAAUCA GUCGAAGAUA C CAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACGU AUACGGUGUG ACGCCUGCCC GG UGCCGGG AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUGAUC GAAGCCCCGG UAAACGGCGG CCGUAACUAU AAC GGUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCUGCA CGAAUGGCGU AAUGAUGGCC AGGCUGUCUC CACC CGAGA CUCAGUGAAA UUGAACUCGC UGUGAAGAUG CAGUGUACCC GCGGCAAGAC GGAAAGACCC CGUAAACCUU UACUA UAGC UUGACACUGA ACAUUGAGCC UUGAUGUGUA GGAUAGGUGG GAGGCUUUGA AGUGUGGACG CCAGUCUGCA UGGAGC CGA CCUUGAAAUA CCACCCUUUA AUGUUUGAUG UUCUAACGUU GACCCGUAAU CCGGGUUGCG GACAGUGUCU GGUGGGU AG UUUGACUGGG GCGGUCUCCU CCUAAAGAGU AACGGAGGAG CACGAAGGUU GGCUAAUCCU GGUCGGACAU CAGGAGGU U AGUGCAAUGG CAUAAGCCAG CUUGACUGCG AGCGUGACGG CGCGAGCAGG UGCGAAAGCA GGUCAUAGUG AUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCGGGGAUA ACAGGCUGAU ACCGCCCAAG AGUUCAUAUC GACGGCGGU GUUUGGCACC UCGAUGUCGG CUCAUCACAU CCUGGGGCUG AAGUAGGUCC CAAGGGUAUG GCUGUUCGCC A UUUAAAGU GGUACGCGAG CUGGGUUUAG AACGUCGUGA GACAGUUCGG UCCCUAUCUG CCGUGGGCGC UGGAGAACUG AG GGGGGCU GCUCCUAGUA CGAGAGGACC GGAGUGGACG CAUCACUGGU GUUCGGGUUG UCAUGCCAAU GGCACUGCCC GGU AGCUAA AUGCGGAAGA GAUAAGUGCU GAAAGCAUCU AAGCACGAAA CUUGCCCCGA GAUGAGUUCU CCCUGACCCU UUAA GGGUC CUGAAGGAAC GUUGAAGACG ACGACGUUGA UAGGCCGGGU GUGUAAGCGC AGCGAUGCGU UGAGCUAACC GGUAC UAAU GAACCGUGAG GCUUAACCU

+
Macromolecule #8: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 8 / Number of copies: 2
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 38.813133 KDa
SequenceString:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCU CCCCAUGCGA GAGUAGGGAA CUGCCAGGCA A

+
Macromolecule #32: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 32 / Number of copies: 2
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 498.725406 KDa
SequenceString: AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC ...String:
AAUUGAAGAG UUUGAUCAUG GCUCAGAUUG AACGCUGGCG GCAGGCCUAA CACAUGCAAG UCGAACGGUA ACAGGAAGAA GCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA A ACGGUAGC UAAUACCGCA UAACGUCGCA AGACCAAAGA GGGGGACCUU CGGGCCUCUU GCCAUCGGAU GUGCCCAGAU GG GAUUAGC UAGUAGGUGG GGUAACGGCU CACCUAGGCG ACGAUCCCUA GCUGGUCUGA GAGGAUGACC AGCCACACUG GAA CUGAGA CACGGUCCAG ACUCCUACGG GAGGCAGCAG UGGGGAAUAU UGCACAAUGG GCGCAAGCCU GAUGCAGCCA UGCC GCGUG UAUGAAGAAG GCCUUCGGGU UGUAAAGUAC UUUCAGCGGG GAGGAAGGGA GUAAAGUUAA UACCUUUGCU CAUUG ACGU UACCCGCAGA AGAAGCACCG GCUAACUCCG UGCCAGCAGC CGCGGUAAUA CGGAGGGUGC AAGCGUUAAU CGGAAU UAC UGGGCGUAAA GCGCACGCAG GCGGUUUGUU AAGUCAGAUG UGAAAUCCCC GGGCUCAACC UGGGAACUGC AUCUGAU AC UGGCAAGCUU GAGUCUCGUA GAGGGGGGUA GAAUUCCAGG UGUAGCGGUG AAAUGCGUAG AGAUCUGGAG GAAUACCG G UGGCGAAGGC GGCCCCCUGG ACGAAGACUG ACGCUCAGGU GCGAAAGCGU GGGGAGCAAA CAGGAUUAGA UACCCUGGU AGUCCACGCC GUAAACGAUG UCGACUUGGA GGUUGUGCCC UUGAGGCGUG GCUUCCGGAG CUAACGCGUU AAGUCGACCG CCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU U CGAUGCAA CGCGAAGAAC CUUACCUGGU CUUGACAUCC ACGGAAGUUU UCAGAGAUGA GAAUGUGCCU UCGGGAACCG UG AGACAGG UGCUGCAUGG CUGUCGUCAG CUCGUGUUGU GAAAUGUUGG GUUAAGUCCC GCAACGAGCG CAACCCUUAU CCU UUGUUG CCAGCGGUCC GGCCGGGAAC UCAAAGGAGA CUGCCAGUGA UAAACUGGAG GAAGGUGGGG AUGACGUCAA GUCA UCAUG GCCCUUACGA CCAGGGCUAC ACACGUGCUA CAAUGGCGCA UACAAAGAGA AGCGACCUCG CGAGAGCAAG CGGAC CUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAG AAU GCCACGGUGA AUACGUUCCC GGGCCUUGUA CACACCGCCC GUCACACCAU GGGAGUGGGU UGCAAAAGAA GUAGGUA GC UUAACCUUCG GGAGGGCGCU UACCACUUUG UGAUUCAUGA CUGGGGUGAA GUCGUAACAA GGUAACCGUA GGGGAACC U GCGGUUGGAU CACCUCCU

+
Macromolecule #56: tRNA Mixture

MacromoleculeName: tRNA Mixture / type: rna / ID: 56 / Number of copies: 2
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Molecular weightTheoretical: 24.77177 KDa
SequenceString:
CGCGGGGUGG AGCAGCCUGG UAGCUCGUCU GGCUCAUAAC CAGAAGAUCG UCGGUUCAAA UCCGGCCCCC GCAACCA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.15 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 18000
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6h58:
Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome

+
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