[English] 日本語
Yorodumi
- EMDB-20638: E. coli 50S with phazolicin (PHZ) bound in exit tunnel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20638
TitleE. coli 50S with phazolicin (PHZ) bound in exit tunnel
Map dataCharge density map used for real space refine, obtained as described by Wang, J. (2017)
Sample
  • Complex: E. coli ribosome with phazolicin in exit tunnel
    • Complex: E. coli 50S
      • RNA: x 2 types
      • Protein or peptide: x 29 types
    • Complex: Phazolicin
      • Protein or peptide: x 1 types
Keywordsribosome / phazolicin / antimicrobial protein / RIBOSOME-INHIBITOR complex
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribosomal large subunit assembly / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site ...Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 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 L11, N-terminal / 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 protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / 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 L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, N-terminal
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / : / Large ribosomal subunit protein bL36 / 50S ribosomal protein L24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL2 / 50S ribosomal protein L3 / Large ribosomal subunit protein bL27 ...Large ribosomal subunit protein uL15 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / : / Large ribosomal subunit protein bL36 / 50S ribosomal protein L24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL2 / 50S ribosomal protein L3 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L21 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / Large ribosomal subunit protein uL29 / 50S ribosomal protein L23 / 50S ribosomal protein L11 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L18 / 50S ribosomal protein L16 / 50S ribosomal protein L19 / 50S ribosomal protein L33 / Large ribosomal subunit protein bL32 / 50S ribosomal protein L28 / 50S ribosomal protein L5
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Rhizobium sp. Pop5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsWatson ZL / Cate JHD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM R01-114454 United States
National Science Foundation (NSF, United States)1106400 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.
Authors: Dmitrii Y Travin / Zoe L Watson / Mikhail Metelev / Fred R Ward / Ilya A Osterman / Irina M Khven / Nelli F Khabibullina / Marina Serebryakova / Peter Mergaert / Yury S Polikanov / Jamie H D ...Authors: Dmitrii Y Travin / Zoe L Watson / Mikhail Metelev / Fred R Ward / Ilya A Osterman / Irina M Khven / Nelli F Khabibullina / Marina Serebryakova / Peter Mergaert / Yury S Polikanov / Jamie H D Cate / Konstantin Severinov /
Abstract: Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides ...Ribosome-synthesized post-translationally modified peptides (RiPPs) represent a rapidly expanding class of natural products with various biological activities. Linear azol(in)e-containing peptides (LAPs) comprise a subclass of RiPPs that display outstanding diversity of mechanisms of action while sharing common structural features. Here, we report the discovery of a new LAP biosynthetic gene cluster in the genome of Rhizobium Pop5, which encodes the precursor peptide and modification machinery of phazolicin (PHZ) - an extensively modified peptide exhibiting narrow-spectrum antibacterial activity against some symbiotic bacteria of leguminous plants. The cryo-EM structure of the Escherichia coli 70S-PHZ complex reveals that the drug interacts with the 23S rRNA and uL4/uL22 proteins and obstructs ribosomal exit tunnel in a way that is distinct from other compounds. We show that the uL4 loop sequence determines the species-specificity of antibiotic action. PHZ expands the known diversity of LAPs and may be used in the future as biocontrol agent for agricultural needs.
History
DepositionAug 23, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6u48
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20638.png

Downloads & links

-
Map

FileDownload / File: emd_20638.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCharge density map used for real space refine, obtained as described by Wang, J. (2017)
Voxel sizeX=Y=Z: 1.1136 Å
Density
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.14081855 - 0.21396987
Average (Standard dev.)-0.00000004051004 (±0.0077487044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-84-54-90
Dimensions320320320
Spacing320320320
CellA=B=C: 356.352 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11361.11361.1136
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z356.352356.352356.352
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ254265109
MAP C/R/S123
start NC/NR/NS-54-84-90
NC/NR/NS320320320
D min/max/mean-0.1410.214-0.000

-
Supplemental data

-
Mask #1

Fileemd_20638_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION post-processed map, used for preview image

Fileemd_20638_additional_1.map
AnnotationRELION post-processed map, used for preview image
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RELION 3D auto-refine map

Fileemd_20638_additional_2.map
AnnotationRELION 3D auto-refine map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map #1

Fileemd_20638_half_map_1.map
Annotationhalf map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map #2

Fileemd_20638_half_map_2.map
Annotationhalf map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : E. coli ribosome with phazolicin in exit tunnel

EntireName: E. coli ribosome with phazolicin in exit tunnel
Components
  • Complex: E. coli ribosome with phazolicin in exit tunnel
    • Complex: E. coli 50S
      • RNA: 23S rRNA23S ribosomal RNA
      • RNA: 5S rRNA5S ribosomal RNA
      • Protein or peptide: 50S ribosomal protein uL2
      • Protein or peptide: 50S ribosomal protein uL3
      • Protein or peptide: 50S ribosomal protein uL4
      • Protein or peptide: 50S ribosomal protein uL5
      • Protein or peptide: 50S ribosomal protein uL6
      • Protein or peptide: 50S ribosomal protein bL9
      • Protein or peptide: 50S ribosomal protein uL11
      • Protein or peptide: 50S ribosomal protein uL13
      • Protein or peptide: 50S ribosomal protein uL14
      • Protein or peptide: 50S ribosomal protein uL15
      • Protein or peptide: 50S ribosomal protein uL16
      • Protein or peptide: 50S ribosomal protein bL17
      • Protein or peptide: 50S ribosomal protein uL18
      • Protein or peptide: 50S ribosomal protein bL19
      • Protein or peptide: 50S ribosomal protein bL20
      • Protein or peptide: 50S ribosomal protein bL21
      • Protein or peptide: 50S ribosomal protein uL22
      • Protein or peptide: 50S ribosomal protein uL23
      • Protein or peptide: 50S ribosomal protein uL24
      • Protein or peptide: 50S ribosomal protein bL25
      • Protein or peptide: 50S ribosomal protein bL27
      • Protein or peptide: 50S ribosomal protein bL28
      • Protein or peptide: 50S ribosomal protein uL29
      • Protein or peptide: 50S ribosomal protein uL30
      • Protein or peptide: 50S ribosomal protein bL32
      • Protein or peptide: 50S ribosomal protein bL33
      • Protein or peptide: 50S ribosomal protein bL34
      • Protein or peptide: 50S ribosomal protein bL35
      • Protein or peptide: 50S ribosomal protein bL36
    • Complex: Phazolicin
      • Protein or peptide: phazolicin

+
Supramolecule #1: E. coli ribosome with phazolicin in exit tunnel

SupramoleculeName: E. coli ribosome with phazolicin in exit tunnel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Ribosomal small subunit is not modeled due to poor density in reconstruction

+
Supramolecule #2: E. coli 50S

SupramoleculeName: E. coli 50S / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#31
Source (natural)Organism: Escherichia coli (E. coli)

+
Supramolecule #3: Phazolicin

SupramoleculeName: Phazolicin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #32
Source (natural)Organism: Rhizobium sp. Pop5 (bacteria)

+
Macromolecule #1: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 941.092125 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 AAU(1MG)(PSU)(5MU)GAAA AAUUAGCGGA UGACUUGUGG CUGGGGGUGA AAGGCCA AU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACU G UUUCGGCAAG GGGGUC(N)(N)(N)(N) (N)(N)ACUUACCA ACCCGAUGCA AACUGCGAAU ACCGGAGAAU GUUAUCA CG GGAGACACAC GGCGGG(PSU)GCU AACGUCCGUC GUGAAGAGGG AAACAACCCA GACCGCCAGC UAAGGUCCCA AAGU CAUGG UUAAGUGGGA AACGAUGUGG GAAGGCCCAG ACAGCCAGGA UGUUGGCUUA GAAGCAGCCA UCAUUUAAAG AAAGC GUAA UAGCUCACUG GUCGAGUCGG CCUGCGCGGA AGAUGUAACG GGGCUAAACC AUGCACCGAA GCUGCGGCAG CGACGC UUA UGCGUUGUUG GGUAGGGGAG CGUUCUGUAA GCCUGCGAAG GUGUGCUGUG AGGCAUGCUG GAGGUAUCAG AAGUGCG AA UGCUGACAUA AGUAACGAUA AAGCGGGUGA AAAGCCCGCU CGCCGGAAGA CCAAGGGUUC CUGUCCAACG UUAAUCGG G GCAGGGUGAG UCGACCCCUA AGGCGAGGCC GAAAGGCGUA GUCGAUGGGA AACAGGUUAA UAUUCCUGUA CUUGGUGUU ACUGCGAAGG GGGGACGGAG AAGGCUAUGU UGGCCGGGCG ACGGUUGUCC CGGUUUAAGC GUGUAGGCUG GUUUUCCAGG CAAAUCCGG AAAAUCAAGG CUGAGGCGUG AUGACGAGGC ACUACGGUGC UGAAGCAACA AAUGCCCUGC UUCCAGGAAA A GCCUCUAA GCAUCAGGUA ACAUCAAAUC GUACCCCAAA CCGACAC(6MZ)GG UGGUCAGGUA GAGAAUACCA AGGCGCUU G AGAGAACUCG GGUGAAGGAA CUAGGCAAAA UGGUGCCGUA ACUUCGGGAG AAGGCACGCU GAUAUGUAGG UGAGGUCCC UCGCGGAUGG AGCUGAAAUC AGUCGAAGAU ACCAGCUGGC UGCAACUGUU UAUUAAAAAC ACAGCACUGU GCAAACACGA AAGUGGACG UAUACGGUGU GACGCCU(2MG)CC CGGUGCCGGA AGGUUAAUUG AUGGGGUUAG CGCAAGCGAA GCUCUUG AU CGAAGCCCCG GUAAACGGCG GCCG(PSU)AAC(3TD)A (PSU)AACGGUCCU AAGGUAGCGA AA(5MU)UCCUUGU CG GGUAAGU UCCGAC(5MC)UGC ACGAAUGGCG UAAUGAUGGC CAGGCUGUCU CCACCCGAGA CUCAGUGAAA UUGAACUCG CUGUG(6MZ)AGAU GCAGUGUACC CGCGGCAAGA CGGAAAGACC CCGU(G7M)AACCU UUACUAUAGC UUGACACUGA AC AUUGAGC CUUGAUGUGU AGGAUAGGUG GGAGGCUUUG AAGUGUGGAC GCCAGUCUGC AUGGAGCCGA CCUUGAAAUA CCA CCCUUU AAUGUUUGAU GUUCUAACGU UGACCCGUAA UCCGGGUUGC GGACAGUGUC UGGUGGGUAG UUUGACUG(OMG)G GCGGUCUCC UCCUAAAGAG UAACGGAGGA GCACGAAGGU UGGCUAAUCC UGGUCGGACA UCAGGAGGUU AGUGCAAUGG C AUAAGCCA GCUUGACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AA GGGCCAU CGCUCAACGG AUAAAAGGUA CUCCG(2MG)GGA(H2U) AACAGGC(PSU)GA UACCGCCCAA GAGUUCAUAU C GACGGCGG UGUUUGGCA(OMC) CUCG(2MA)(PSU)GUCG GCUCAUCACA UCCUGGGGCU GAAGUAGGUC CCAAGGGUAU GGC(OMU)GUUCG CCAUUUAAAG UGGUACGCGA GC(PSU)GGGUUUA GAACGUCGUG AGACAGU(PSU)CG GUCCCUAUC UGCCGUGGGC GCUGGAGAAC UGAGGGGGGC UGCUCCUAGU ACGAGAGGAC CGGAGUGGAC GCAUCACUGG UGUUCGGGUU GUCAUGCCA AUGGCACUGC CCGGUAGCUA AAUGCGGAAG AGAUAAGUGC UGAAAGCAUC UAAGCACGAA ACUUGCCCCG A GAUGAGUU CUCCCUGACC CUUUAAGGGU CCUGAAGGAA CGUUGAAGAC GACGACGUUG AUAGGCCGGG UGUGUAAGCG CA GCGAUGC GUUGAGCUAA CCGGUACUAA UGAACCGUGA GGCUUAACCU U

+
Macromolecule #2: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 38.177762 KDa
SequenceString:
GCCUGGCGGC CGUAGCGCGG UGGUCCCACC UGACCCCAUG CCGAACUCAG AAGUGAAACG CCGUAGCGCC GAUGGUAGUG UGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCA

GENBANK: GENBANK: CP023870.1

+
Macromolecule #3: 50S ribosomal protein uL2

MacromoleculeName: 50S ribosomal protein uL2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
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

UniProtKB: Large ribosomal subunit protein uL2

+
Macromolecule #4: 50S ribosomal protein uL3

MacromoleculeName: 50S ribosomal protein uL3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.291562 KDa
SequenceString: MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN (MEQ)TPGKVF KG KKMAGQMGNE ...String:
MIGLVGKKVG MTRIFTEDGV SIPVTVIEVE ANRVTQVKDL ANDGYRAIQV TTGAKKANRV TKPEAGHFAK AGVEAGRGLW EFRLAEGEE FTVGQSISVE LFADVKKVDV TGTSKGKGFA GTVKRWNFRT QDATHGNSLS HRVPGSIGQN (MEQ)TPGKVF KG KKMAGQMGNE RVTVQSLDVV RVDAERNLLL VKGAVPGATG SDLIVKPAVK A

UniProtKB: 50S ribosomal protein L3

+
Macromolecule #5: 50S ribosomal protein uL4

MacromoleculeName: 50S ribosomal protein uL4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
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

UniProtKB: 50S ribosomal protein L4

+
Macromolecule #6: 50S ribosomal protein uL5

MacromoleculeName: 50S ribosomal protein uL5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
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

UniProtKB: 50S ribosomal protein L5

+
Macromolecule #7: 50S ribosomal protein uL6

MacromoleculeName: 50S ribosomal protein uL6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
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

UniProtKB: 50S ribosomal protein L6

+
Macromolecule #8: 50S ribosomal protein bL9

MacromoleculeName: 50S ribosomal protein bL9 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.78902 KDa
SequenceString:
MQVILLDKVA NLGSLGDQVN VKAGYARNFL VPQGKAVPAT KKNIEFFEAR RAELEAKLAE VLAAANARAE KINALETVTI ASKAGDEGK LFGSIGTRDI ADAVTAAGVE VAKSEVRLPN GVLRTTGEHE VSFQVHSEVF AKVIVNVVAE

UniProtKB: 50S ribosomal protein L9

+
Macromolecule #9: 50S ribosomal protein uL11

MacromoleculeName: 50S ribosomal protein uL11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.020303 KDa
SequenceString:
YVKLQVAAGM ANPSPPVGPA LGQQGVNIME FCKAFNAKTD SIEKGLPIPV VITVYADRSF TFVTKTPPAA VLLKKAAGIK SGSGKPNKD KVGKISRAQL QEIAQTKAAD MTGADIEAMT RSIEGTARSM GLVVE

UniProtKB: 50S ribosomal protein L11

+
Macromolecule #10: 50S ribosomal protein uL13

MacromoleculeName: 50S ribosomal protein uL13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.050606 KDa
SequenceString:
MKTFTAKPET VKRDWYVVDA TGKTLGRLAT ELARRLRGKH KAEYTPHVDT GDYIIVLNAD KVAVTGNKRT DKVYYHHTGH IGGIKQATF EEMIARRPER VIEIAVKGML PKGPLGRAMF RKLKVYAGNE HNHAAQQPQV LDI

UniProtKB: 50S ribosomal protein L13

+
Macromolecule #11: 50S ribosomal protein uL14

MacromoleculeName: 50S ribosomal protein uL14 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.45191 KDa
SequenceString:
MIQEQTMLNV ADNSGARRVM CIKVLGGSHR RYAGVGDIIK ITIKEAIPRG KVKKGDVLKA VVVRTKKGVR RPDGSVIRFD GNACVLLNN NSEQPIGTRI FGPVTRELRS EKFMKIISLA PEV

UniProtKB: Large ribosomal subunit protein uL14

+
Macromolecule #12: 50S ribosomal protein uL15

MacromoleculeName: 50S ribosomal protein uL15 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.008471 KDa
SequenceString:
MRLNTLSPAE GSKKAGKRLG RGIGSGLGKT GGRGHKGQKS RSGGGVRRGF EGGQMPLYRR LPKFGFTSRK AAITAEIRLS DLAKVEGGV VDLNTLKAAN IIGIQIEFAK VILAGEVTTP VTVRGLRVTK GARAAIEAAG GKIEE

UniProtKB: Large ribosomal subunit protein uL15

+
Macromolecule #13: 50S ribosomal protein uL16

MacromoleculeName: 50S ribosomal protein uL16 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.327261 KDa
SequenceString:
MLQPKRTKFR KMHKGRNRGL AQGTDVSFGS FGLKAVGRGR LTARQIEAAR RAMTRAVKRQ GKIWIRVFPD KPITEKPLAV (4D4)MGKGKGNV EYWVALIQPG KVLYEMDGVP EELAREAFKL AAAKLPIKTT FVTKTVM

UniProtKB: 50S ribosomal protein L16

+
Macromolecule #14: 50S ribosomal protein bL17

MacromoleculeName: 50S ribosomal protein bL17 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.721938 KDa
SequenceString:
MRHRKSGRQL NRNSSHRQAM FRNMAGSLVR HEIIKTTLPK AKELRRVVEP LITLAKTDSV ANRRLAFART RDNEIVAKLF NELGPRFAS RAGGYTRILK CGFRAGDNAP MAYIELVDRS E

UniProtKB: UNIPROTKB: A0A0A8UJP9

+
Macromolecule #15: 50S ribosomal protein uL18

MacromoleculeName: 50S ribosomal protein uL18 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.663471 KDa
SequenceString:
DKKSARIRRA TRARRKLQEL GATRLVVHRT PRHIYAQVIA PNGSEVLVAA STVEKAIAEQ LKYTGNKDAA AAVGKAVAER ALEKGIKDV SFDRSGFQYH GRVQALADAA REAGLQF

UniProtKB: 50S ribosomal protein L18

+
Macromolecule #16: 50S ribosomal protein bL19

MacromoleculeName: 50S ribosomal protein bL19 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.028082 KDa
SequenceString:
SNIIKQLEQE QMKQDVPSFR PGDTVEVKVW VVEGSKKRLQ AFEGVVIAIR NRGLHSAFTV RKISNGEGVE RVFQTHSPVV DSISVKRRG AVRKAKLYYL RERTGKAARI KERLN

UniProtKB: 50S ribosomal protein L19

+
Macromolecule #17: 50S ribosomal protein bL20

MacromoleculeName: 50S ribosomal protein bL20 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.396828 KDa
SequenceString:
ARVKRGVIAR ARHKKILKQA KGYYGARSRV YRVAFQAVIK AGQYAYRDRR QRKRQFRQLW IARINAAARQ NGISYSKFIN GLKKASVEI DRKILADIAV FDKVAFTALV EKAKAALA

UniProtKB: 50S ribosomal protein L20

+
Macromolecule #18: 50S ribosomal protein bL21

MacromoleculeName: 50S ribosomal protein bL21 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.586374 KDa
SequenceString:
MYAVFQSGGK QHRVSEGQTV RLEKLDIATG ETVEFAEVLM IANGEEVKIG VPFVDGGVIK AEVVAHGRGE KVKIVKFRRR KHYRKQQGH RQWFTDVKIT GISA

UniProtKB: 50S ribosomal protein L21

+
Macromolecule #19: 50S ribosomal protein uL22

MacromoleculeName: 50S ribosomal protein uL22 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.253359 KDa
SequenceString:
METIAKHRHA RSSAQKVRLV ADLIRGKKVS QALDILTYTN KKAAVLVKKV LESAIANAEH NDGADIDDLK VTKIFVDEGP SMKRIMPRA KGRADRILKR TSHITVVVSD R

UniProtKB: 50S ribosomal protein L22

+
Macromolecule #20: 50S ribosomal protein uL23

MacromoleculeName: 50S ribosomal protein uL23 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.546472 KDa
SequenceString:
MIREERLLKV LRAPHVSEKA STAMEKSNTI VLKVAKDATK AEIKAAVQKL FEVEVEVVNT LVVKGKVKRH GQRIGRRSDW KKAYVTLKE GQNL

UniProtKB: 50S ribosomal protein L23

+
Macromolecule #21: 50S ribosomal protein uL24

MacromoleculeName: 50S ribosomal protein uL24 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.078874 KDa
SequenceString:
AAKIRRDDEV IVLTGKDKGK RGKVKNVLSS GKVIVEGINL VKKHQKPVPA LNQPGGIVEK EAAIQVSNVA IFNAATGKAD RVGFRFEDG KKVRFFKSNS ETI

UniProtKB: 50S ribosomal protein L24

+
Macromolecule #22: 50S ribosomal protein bL25

MacromoleculeName: 50S ribosomal protein bL25 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.713465 KDa
SequenceString:
MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV LTIVVDGKEI KVKAQDVQRH PYKPKLQHI DFVRA

UniProtKB: Large ribosomal subunit protein bL25

+
Macromolecule #23: 50S ribosomal protein bL27

MacromoleculeName: 50S ribosomal protein bL27 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.174394 KDa
SequenceString:
RNGRDSEAKR LGVKRFGGES VLAGSIIVRQ RGTKFHAGAN VGCGRDHTLF AKADGKVKFE VKGPKNRKFI SIEAE

UniProtKB: Large ribosomal subunit protein bL27

+
Macromolecule #24: 50S ribosomal protein bL28

MacromoleculeName: 50S ribosomal protein bL28 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.896354 KDa
SequenceString:
SRVCQVTGKR PVTGNNRSHA LNATKRRFLP NLHSHRFWVE SEKRFVTLRV SAKGMRVIDK KGIDTVLAEL RARGEKY

UniProtKB: 50S ribosomal protein L28

+
Macromolecule #25: 50S ribosomal protein uL29

MacromoleculeName: 50S ribosomal protein uL29 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.155267 KDa
SequenceString:
KAKELREKSV EELNTELLNL LREQFNLRMQ AASGQLQQSH LLKQVRRDVA RVKTLLNEKA GA

UniProtKB: Large ribosomal subunit protein uL29

+
Macromolecule #26: 50S ribosomal protein uL30

MacromoleculeName: 50S ribosomal protein uL30 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.423625 KDa
SequenceString:
AKTIKITQTR SAIGRLPKHK ATLLGLGLRR IGHTVEREDT PAIRGMINAV SFMVKVEE

UniProtKB: 50S ribosomal protein L30

+
Macromolecule #27: 50S ribosomal protein bL32

MacromoleculeName: 50S ribosomal protein bL32 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 6.332249 KDa
SequenceString:
AVQQNKPTRS KRGMRRSHDA LTAVTSLSVD KTSGEKHLRH HITADGYYRG RKVIAK

UniProtKB: Large ribosomal subunit protein bL32

+
Macromolecule #28: 50S ribosomal protein bL33

MacromoleculeName: 50S ribosomal protein bL33 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.814842 KDa
SequenceString:
GIREKIKLVS SAGTGHFYTT TKNKRTKPEK LELKKFDPVV RQHVIYKEAK

UniProtKB: 50S ribosomal protein L33

+
Macromolecule #29: 50S ribosomal protein bL34

MacromoleculeName: 50S ribosomal protein bL34 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.397463 KDa
SequenceString:
MKRTFQPSVL KRNRSHGFRA RMATKNGRQV LARRRAKGRA RLTVSK

UniProtKB: Large ribosomal subunit protein bL34

+
Macromolecule #30: 50S ribosomal protein bL35

MacromoleculeName: 50S ribosomal protein bL35 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 7.181835 KDa
SequenceString:
PKIKTVRGAA KRFKKTGKGG FKHKHANLRH ILTKKATKRK RHLRPKAMVS KGDLGLVIAC LPYA

UniProtKB: 50S ribosomal protein L35

+
Macromolecule #31: 50S ribosomal protein bL36

MacromoleculeName: 50S ribosomal protein bL36 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 4.37739 KDa
SequenceString:
MKVRASVKKL CRNCKIVKRD GVIRVICSAE PKHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

+
Macromolecule #32: phazolicin

MacromoleculeName: phazolicin / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhizobium sp. Pop5 (bacteria)
Molecular weightTheoretical: 2.054102 KDa
SequenceString:
T(BB9)AR(BB9)DS(A0G)SR (BB9)GA(A0G)GK(A0G)SG(A0G) AS

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ybb

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 65393
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4ybb


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6u48:
E. coli 50S with phazolicin (PHZ) bound in exit tunnel

+
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