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- EMDB-51964: Complex 1 30S-IF1-IF2-IF3-GE81112 -

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Basic information

Entry
Database: EMDB / ID: EMD-51964
TitleComplex 1 30S-IF1-IF2-IF3-GE81112
Map dataComplex 1 30S-IF1-IF2-IF3-GE81112 Full map
Sample
  • Complex: Complex 1 30S-IF1-IF2-IF3-GE81112
    • RNA: x 3 types
    • Protein or peptide: x 23 types
  • Ligand: x 4 types
KeywordsAntibiotic / initiation factor / GE81112 / 30S / RIBOSOME
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability ...ribosome disassembly / guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / translation initiation factor activity / mRNA regulatory element binding translation repressor activity / response to cold / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosome biogenesis / regulation of translation / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / GTP binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor 3 ...Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Putative DNA-binding domain superfamily / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Elongation factor Tu domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / Ribosomal protein S21 superfamily / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / : / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature.
Similarity search - Domain/homology
Translation initiation factor IF-2 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-3 / 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 ...Translation initiation factor IF-2 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-3 / 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 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSchedlbauer A / Han X / van Bakel W / Kaminishi T / Ochoa-Lizarralde B / Iturrioz I / Capuni R / Parry R / Zegarra R / Gil-Carton D ...Schedlbauer A / Han X / van Bakel W / Kaminishi T / Ochoa-Lizarralde B / Iturrioz I / Capuni R / Parry R / Zegarra R / Gil-Carton D / Lopez-Alonso JP / Barragan Sanz K / Brandi L / Gualerzi CO / Fucini P / Connell SR
Funding support Spain, 1 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-122705OB-I00 Spain
CitationJournal: bioRxiv / Year: 2024
Title: A binding site for the antibiotic GE81112 in the ribosomal mRNA channel.
Authors: Andreas Schedlbauer / Xu Han / Wouter van Bakel / Tatsuya Kaminishi / Borja Ochoa-Lizarralde / Idoia Iturrioz / Retina Çapuni / Ransford Parry / Ronny Zegarra / David Gil-Carton / Jorge P ...Authors: Andreas Schedlbauer / Xu Han / Wouter van Bakel / Tatsuya Kaminishi / Borja Ochoa-Lizarralde / Idoia Iturrioz / Retina Çapuni / Ransford Parry / Ronny Zegarra / David Gil-Carton / Jorge P López-Alonso / Kristina Barragan Sanz / Letizia Brandi / Claudio O Gualerzi / Paola Fucini / Sean R Connell /
Abstract: The initiation phase is the rate-limiting step of protein synthesis (translation) and is finely regulated, making it an important drug target. In bacteria, initiation is guided by three initiation ...The initiation phase is the rate-limiting step of protein synthesis (translation) and is finely regulated, making it an important drug target. In bacteria, initiation is guided by three initiation factors and involves positioning the start site on the messenger RNA within the P-site on the small ribosomal subunit (30S), where it is decoded by the initiator tRNA. This process can be efficiently inhibited by GE81112, a natural hydrophilic, noncyclic, nonribosomal tetrapeptide. It is found in nature in three structural variants (A, B and B1 with molecular masses of 643-658 Da). Previous biochemical and structural characterisation of GE81112 indicates that the primary mechanism of action of this antibiotic is to (1) prevent the initiator tRNA from binding correctly to the P-site and (2) block conformational rearrangements in initiation factor IF3, resulting in an 30S pre/C state. In this study, using cryoEM, we have determined the binding site of GE81112 in initiation complexes (3.2-3.7Å) and on empty ribosomes (2.09 Å). This binding site is within the mRNA channel (E-site) but remote from the binding site of the initiation factors and initiator tRNA. This suggests that it acts allosterically to prevent the initiator tRNA from being locked into place. The binding mode is consistent with previous biochemical studies and recent work identifying the key pharmacophores of GE81112.
History
DepositionOct 31, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51964.png

Downloads & links

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Map

FileDownload / File: emd_51964.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex 1 30S-IF1-IF2-IF3-GE81112 Full map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 325.8 Å		1.09 Å/pix.
x 300 pix.
= 325.8 Å		1.09 Å/pix.
x 300 pix.
= 325.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.086 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.012278563 - 0.037410703
Average (Standard dev.)0.000067826964 (±0.0020761932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 325.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51964_msk_1.map
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Additional map: Complex 1 30S-IF1-IF2-IF3-GE81112 sharpened

Fileemd_51964_additional_1.map
AnnotationComplex 1 30S-IF1-IF2-IF3-GE81112 sharpened
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Half map: Complex 1 30S-IF1-IF2-IF3-GE81112 half map

Fileemd_51964_half_map_1.map
AnnotationComplex 1 30S-IF1-IF2-IF3-GE81112 half map
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Half map: Complex 1 30S-IF1-IF2-IF3-GE81112 half map

Fileemd_51964_half_map_2.map
AnnotationComplex 1 30S-IF1-IF2-IF3-GE81112 half map
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Sample components

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Entire : Complex 1 30S-IF1-IF2-IF3-GE81112

EntireName: Complex 1 30S-IF1-IF2-IF3-GE81112
Components
  • Complex: Complex 1 30S-IF1-IF2-IF3-GE81112
    • RNA: mRNA (5'-R(P*AP*AP*UP*G)-3')
    • RNA: t-RNA (77-MER)
    • RNA: 16S RNA (1534-MER)
    • Protein or peptide: Small ribosomal subunit protein uS2
    • Protein or peptide: Small ribosomal subunit protein uS3
    • Protein or peptide: Small ribosomal subunit protein uS4
    • Protein or peptide: Small ribosomal subunit protein uS5
    • Protein or peptide: Small ribosomal subunit protein bS6, fully modified isoform
    • Protein or peptide: Small ribosomal subunit protein uS7
    • Protein or peptide: Small ribosomal subunit protein uS8
    • Protein or peptide: Small ribosomal subunit protein uS9
    • Protein or peptide: Small ribosomal subunit protein uS10
    • Protein or peptide: Small ribosomal subunit protein uS11
    • Protein or peptide: Small ribosomal subunit protein uS12
    • Protein or peptide: Small ribosomal subunit protein uS13
    • Protein or peptide: Small ribosomal subunit protein uS14
    • Protein or peptide: Small ribosomal subunit protein uS15
    • Protein or peptide: Small ribosomal subunit protein bS16
    • Protein or peptide: Small ribosomal subunit protein uS17
    • Protein or peptide: Small ribosomal subunit protein bS18
    • Protein or peptide: Small ribosomal subunit protein uS19
    • Protein or peptide: Small ribosomal subunit protein bS20
    • Protein or peptide: Small ribosomal subunit protein bS21
    • Protein or peptide: Translation initiation factor IF-1
    • Protein or peptide: Translation initiation factor IF-2
    • Protein or peptide: Translation initiation factor IF-3
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl-propanoic acid
  • Ligand: ZINC ION

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Supramolecule #1: Complex 1 30S-IF1-IF2-IF3-GE81112

SupramoleculeName: Complex 1 30S-IF1-IF2-IF3-GE81112 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#26
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: mRNA (5'-R(P*AP*AP*UP*G)-3')

MacromoleculeName: mRNA (5'-R(P*AP*AP*UP*G)-3') / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.264826 KDa
SequenceString:
AAUG

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Macromolecule #2: t-RNA (77-MER)

MacromoleculeName: t-RNA (77-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.838725 KDa
SequenceString:
GGAGCGGUAG UUCAGUCGGU UAGAAUACCG GGCUCAUAAC CCGGGGGUCG CGGGUUCGAG UCCCGUCCGU UCCGCCA

GENBANK: GENBANK: CP093018.1

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Macromolecule #3: 16S RNA (1534-MER)

MacromoleculeName: 16S RNA (1534-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 499.873406 KDa
SequenceString: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUU CUUUGCUGAC GAGUGGCGGA CGGGUGAGUA AUGUCUGGGA AACUGCCUGA UGGAGGGGGA UAACUACUGG A AACGGUAG ...String:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUU CUUUGCUGAC GAGUGGCGGA CGGGUGAGUA AUGUCUGGGA AACUGCCUGA UGGAGGGGGA UAACUACUGG A AACGGUAG CUAAUACCGC AUAACGUCGC AAGACCAAAG AGGGGGACCU UCGGGCCUCU UGCCAUCGGA UGUGCCCAGA UG GGAUUAG CUAGUAGGUG GGGUAACGGC UCACCUAGGC GACGAUCCCU AGCUGGUCUG AGAGGAUGAC CAGCCACACU GGA ACUGAG ACACGGUCCA GACUCCUACG GGAGGCAGCA GUGGGGAAUA UUGCACAAUG GGCGCAAGCC UGAUGCAGCC AUGC CGCGU GUAUGAAGAA GGCCUUCGGG UUGUAAAGUA CUUUCAGCGG GGAGGAAGGG AGUAAAGUUA AUACCUUUGC UCAUU GACG UUACCCGCAG AAGAAGCACC GGCUAACUCC G(PSU)GCCAGCAG CC(G7M)CGGUAAU ACGGAGGGUG CAAGCGUU A AUCGGAAUUA CUGGGCGUAA AGCGCACGCA GGCGGUUUGU UAAGUCAGAU GUGAAAUCCC CGGGCUCAAC CUGGGAACU GCAUCUGAUA CUGGCAAGCU UGAGUCUCGU AGAGGGGGGU AGAAUUCCAG GUGUAGCGGU GAAAUGCGUA GAGAUCUGGA GGAAUACCG GUGGCGAAGG CGGCCCCCUG GACGAAGACU GACGCUCAGG UGCGAAAGCG UGGGGAGCAA ACAGGAUUAG A UACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UA AGUCGAC CGCCUGGGGA GUACGGCCGC AAGGUUAAAA CUCAAAUGAA UUGACGGGGG CCCGCACAAG CGGUGGAGCA UGU GGUUUA AUUCGAU(2MG)(5MC)A ACGCGAAGAA CCUUACCUGG UCUUGACAUC CACGGAAGUU UUCAGAGAUG AGAAUG UGC CUUCGGGAAC CGUGAGACAG GUGCUGCAUG GCUGUCGUCA GCUCGUGUUG UGAAAUGUUG GGUUAAGUCC CGCAACG AG CGCAACCCUU AUCCUUUGUU GCCAGCGGUC CGGCCGGGAA CUCAAAGGAG ACUGCCAGUG AUAAACUGGA GGAAGGUG G GGAUGACGUC AAGUCAUCAU G(2MG)CCCUUACG ACCAGGGCUA CACACGUGCU ACAAUGGCGC AUACAAAGAG AAGCG ACCU CGCGAGAGCA AGCGGACCUC AUAAAGUGCG UCGUAGUCCG GAUUGGAGUC UGCAACUCGA CUCCAUGAAG UCGGAA UCG CUAGUAAUCG UGGAUCAGAA UGCCACGGUG AAUACGUUCC CGGGCCUUGU ACACACCG(4OC)C CGU(5MC)ACACC AUGGGAGUGG GUUGCAAAAG AAGUAGGUAG CUUAACCUUC GGGAGGGCGC UUACCACUUU GUGAUUCAUG ACUGGGGUGA AGUCG(UR3)AAC AAGGUAACCG UAGG(2MG)G(MA6)(MA6)CC UGCGGUUGGA UCACCUCCUU A

GENBANK: GENBANK: CP032808.1

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Macromolecule #4: Small ribosomal subunit protein uS2

MacromoleculeName: Small ribosomal subunit protein uS2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.78167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATVSMRDML KAGVHFGHQT RYWNPKMKPF IFGARNKVHI INLEKTVPMF NEALAELNKI ASRKGKILFV GTKRAASEAV KDAALSCDQ FFVNHRWLGG MLTNWKTVRQ SIKRLKDLET QSQDGTFDKL TKKEALMRTR ELEKLENSLG GIKDMGGLPD A LFVIDADH ...String:
MATVSMRDML KAGVHFGHQT RYWNPKMKPF IFGARNKVHI INLEKTVPMF NEALAELNKI ASRKGKILFV GTKRAASEAV KDAALSCDQ FFVNHRWLGG MLTNWKTVRQ SIKRLKDLET QSQDGTFDKL TKKEALMRTR ELEKLENSLG GIKDMGGLPD A LFVIDADH EHIAIKEANN LGIPVFAIVD TNSDPDGVDF VIPGNDDAIR AVTLYLGAVA ATVREGRSQD LASQAEESFV EA E

UniProtKB: Small ribosomal subunit protein uS2

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Macromolecule #5: Small ribosomal subunit protein uS3

MacromoleculeName: Small ribosomal subunit protein uS3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.031316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGQKVHPNGI RLGIVKPWNS TWFANTKEFA DNLDSDFKVR QYLTKELAKA SVSRIVIERP AKSIRVTIHT ARPGIVIGKK GEDVEKLRK VVADIAGVPA QINIAEVRKP ELDAKLVADS ITSQLERRVM FRRAMKRAVQ NAMRLGAKGI KVEVSGRLGG A EIARTEWY ...String:
MGQKVHPNGI RLGIVKPWNS TWFANTKEFA DNLDSDFKVR QYLTKELAKA SVSRIVIERP AKSIRVTIHT ARPGIVIGKK GEDVEKLRK VVADIAGVPA QINIAEVRKP ELDAKLVADS ITSQLERRVM FRRAMKRAVQ NAMRLGAKGI KVEVSGRLGG A EIARTEWY REGRVPLHTL RADIDYNTSE AHTTYGVIGV KVWIFKGEIL GGMAAVEQPE KPAAQPKKQQ RKGRK

UniProtKB: Small ribosomal subunit protein uS3

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Macromolecule #6: Small ribosomal subunit protein uS4

MacromoleculeName: Small ribosomal subunit protein uS4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.514199 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGEN LLALLEGRLD NVVYRMGFGA TRAEARQLVS HKAIMVNGRV VNIASYQVSP NDVVSIREKA KKQSRVKAAL E LAEQREKP ...String:
MARYLGPKLK LSRREGTDLF LKSGVRAIDT KCKIEQAPGQ HGARKPRLSD YGVQLREKQK VRRIYGVLER QFRNYYKEAA RLKGNTGEN LLALLEGRLD NVVYRMGFGA TRAEARQLVS HKAIMVNGRV VNIASYQVSP NDVVSIREKA KKQSRVKAAL E LAEQREKP TWLEVDAGKM EGTFKRKPER SDLSADINEH LIVELYSK

UniProtKB: Small ribosomal subunit protein uS4

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Macromolecule #7: Small ribosomal subunit protein uS5

MacromoleculeName: Small ribosomal subunit protein uS5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.629398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAHIEKQAGE LQEKLIAVNR VSKTVKGGRI FSFTALTVVG DGNGRVGFGY GKAREVPAAI QKAMEKARRN MINVALNNGT LQHPVKGVH TGSRVFMQPA SEGTGIIAGG AMRAVLEVAG VHNVLAKAYG STNPINVVRA TIDGLENMNS PEMVAAKRGK S VEEILGK

UniProtKB: Small ribosomal subunit protein uS5

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Macromolecule #8: Small ribosomal subunit protein bS6, fully modified isoform

MacromoleculeName: Small ribosomal subunit protein bS6, fully modified isoform
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.727512 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA SPMVKAKDER RERRDDFANE TADDAEAGDS EEEEEE

UniProtKB: Small ribosomal subunit protein bS6

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Macromolecule #9: Small ribosomal subunit protein uS7

MacromoleculeName: Small ribosomal subunit protein uS7 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.055156 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRRRVIGQR KILPDPKFGS ELLAKFVNIL MVDGKKSTAE SIVYSALETL AQRSGKSELE AFEVALENVR PTVEVKSRRV GGSTYQVPV EVRPVRRNAL AMRWIVEAAR KRGDKSMALR LANELSDAAE NKGTAVKKRE DVHRMAEANK AFAHYRWLSL R SFSHQAGA SSKQPALGYL N

UniProtKB: Small ribosomal subunit protein uS7

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Macromolecule #10: Small ribosomal subunit protein uS8

MacromoleculeName: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.146557 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSMQDPIADM LTRIRNGQAA NKAAVTMPSS KLKVAIANVL KEEGFIEDFK VEGDTKPELE LTLKYFQGKA VVESIQRVSR PGLRIYKRK DELPKVMAGL GIAVVSTSKG VMTDRAARQA GLGGEIICYV A

UniProtKB: Small ribosomal subunit protein uS8

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Macromolecule #11: Small ribosomal subunit protein uS9

MacromoleculeName: Small ribosomal subunit protein uS9 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.88627 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAENQYYGTG RRKSSAARVF IKPGNGKIVI NQRSLEQYFG RETARMVVRQ PLELVDMVEK LDLYITVKGG GISGQAGAIR HGITRALME YDESLRSELR KAGFVTRDAR QVERKKVGLR KARRRPQFSK R

UniProtKB: Small ribosomal subunit protein uS9

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Macromolecule #12: Small ribosomal subunit protein uS10

MacromoleculeName: Small ribosomal subunit protein uS10 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.755597 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQNQRIRIRL KAFDHRLIDQ ATAEIVETAK RTGAQVRGPI PLPTRKERFT VLISPHVNKD ARDQYEIRTH LRLVDIVEPT EKTVDALMR LDLAAGVDVQ ISLG

UniProtKB: Small ribosomal subunit protein uS10

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Macromolecule #13: Small ribosomal subunit protein uS11

MacromoleculeName: Small ribosomal subunit protein uS11 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.870975 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKAPIRARK RVRKQVSDGV AHIHASFNNT IVTITDRQGN ALGWATAGGS GFRGSRKSTP FAAQVAAERC ADAVKEYGIK NLEVMVKGP GPGRESTIRA LNAAGFRITN ITDVTPIPHN GCRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11

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Macromolecule #14: Small ribosomal subunit protein uS12

MacromoleculeName: Small ribosomal subunit protein uS12 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.768157 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MATVNQLVRK PRARKVAKSN VPALEACPQK RGVCTRVYTT TPKKPNSALR KVCRVRLTNG FEVTSYIGGE GHNLQEHSVI LIRGGRVKD LPGVRYHTVR GALDCSGVKD RKQARSKYGV KRPKA

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #15: Small ribosomal subunit protein uS13

MacromoleculeName: Small ribosomal subunit protein uS13 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.128467 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGL RHRRGLPVRG QRTKTNARTR KGPRKPIKK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #16: Small ribosomal subunit protein uS14

MacromoleculeName: Small ribosomal subunit protein uS14 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 11.60656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKQSMKARE VKRVALADKY FAKRAELKAI ISDVNASDED RWNAVLKLQT LPRDSSPSRQ RNRCRQTGRP HGFLRKFGLS RIKVREAAM RGEIPGLKKA SW

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #17: Small ribosomal subunit protein uS15

MacromoleculeName: Small ribosomal subunit protein uS15 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.290816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSLSTEATAK IVSEFGRDAN DTGSTEVQVA LLTAQINHLQ GHFAEHKKDH HSRRGLLRMV SQRRKLLDYL KRKDVARYTQ LIERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #18: Small ribosomal subunit protein bS16

MacromoleculeName: Small ribosomal subunit protein bS16 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.207572 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISDR VAALIKEVNK AA

UniProtKB: Small ribosomal subunit protein bS16

+
Macromolecule #19: Small ribosomal subunit protein uS17

MacromoleculeName: Small ribosomal subunit protein uS17 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.724491 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTDKIRTLQG RVVSDKMEKS IVVAIERFVK HPIYGKFIKR TTKLHVHDEN NECGIGDVVE IRECRPLSKT KSWTLVRVVE KAVL

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #20: Small ribosomal subunit protein bS18

MacromoleculeName: Small ribosomal subunit protein bS18 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.005472 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARYFRRRKF CRFTAEGVQE IDYKDIATLK NYITESGKIV PSRITGTRAK YQRQLARAIK RARYLSLLPY TDRHQ

UniProtKB: Small ribosomal subunit protein bS18

+
Macromolecule #21: Small ribosomal subunit protein uS19

MacromoleculeName: Small ribosomal subunit protein uS19 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.455355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRSLKKGPF IDLHLLKKVE KAVESGDKKP LRTWSRRSTI FPNMIGLTIA VHNGRQHVPV FVTDEMVGHK LGEFAPTRTY RGHAADKKA KKK

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #22: Small ribosomal subunit protein bS20

MacromoleculeName: Small ribosomal subunit protein bS20 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.708464 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MANIKSAKKR AIQSEKARKH NASRRSMMRT FIKKVYAAIE AGDKAAAQKA FNEMQPIVDR QAAKGLIHKN KAARHKANLT AQINKLA

UniProtKB: Small ribosomal subunit protein bS20

+
Macromolecule #23: Small ribosomal subunit protein bS21

MacromoleculeName: Small ribosomal subunit protein bS21 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.524039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPVIKVRENE PFDVALRRFK RSCEKAGVLA EVRRREFYEK PTTERKRAKA SAVKRHAKKL ARENARRTRL Y

UniProtKB: Small ribosomal subunit protein bS21

+
Macromolecule #24: Translation initiation factor IF-1

MacromoleculeName: Translation initiation factor IF-1 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 8.26259 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKEDNIEMQ GTVLETLPNT MFRVELENGH VVTAHISGKM RKNYIRILTG DKVTVELTPY DLSKGRIVFR SR

UniProtKB: Translation initiation factor IF-1

+
Macromolecule #25: Translation initiation factor IF-2

MacromoleculeName: Translation initiation factor IF-2 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 97.498164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDVTIKTLA AERQTSVERL VQQFADAGIR KSADDSVSAQ EKQTLIDHLN QKNSGPDKLT LQRKTRSTLN IPGTGGKSKS VQIEVRKKR TFVKRDPQEA ERLAAEEQAQ REAEEQARRE AEESAKREAQ QKAEREAAEQ AKREAAEQAK REAAEKDKVS N QQDDMTKN ...String:
MTDVTIKTLA AERQTSVERL VQQFADAGIR KSADDSVSAQ EKQTLIDHLN QKNSGPDKLT LQRKTRSTLN IPGTGGKSKS VQIEVRKKR TFVKRDPQEA ERLAAEEQAQ REAEEQARRE AEESAKREAQ QKAEREAAEQ AKREAAEQAK REAAEKDKVS N QQDDMTKN AQAEKARREQ EAAELKRKAE EEARRKLEEE ARRVAEEARR MAEENKWTDN AEPTEDSSDY HVTTSQHARQ AE DESDREV EGGRGRGRNA KAARPKKGNK HAESKADREE ARAAVRGGKG GKRKGSSLQQ GFQKPAQAVN RDVVIGETIT VGE LANKMA VKGSQVIKAM MKLGAMATIN QVIDQETAQL VAEEMGHKVI LRRENELEEA VMSDRDTGAA AEPRAPVVTI MGHV DHGKT SLLDYIRSTK VASGEAGGIT QHIGAYHVET ENGMITFLDT PGHAAFTSMR ARGAQATDIV VLVVAADDGV MPQTI EAIQ HAKAAQVPVV VAVNKIDKPE ADPDRVKNEL SQYGILPEEW GGESQFVHVS AKAGTGIDEL LDAILLQAEV LELKAV RKG MASGAVIESF LDKGRGPVAT VLVREGTLHK GDIVLCGFEY GRVRAMRNEL GQEVLEAGPS IPVEILGLSG VPAAGDE VT VVRDEKKARE VALYRQGKFR EVKLARQQKS KLENMFANMT EGEVHEVNIV LKADVQGSVE AISDSLLKLS TDEVKVKI I GSGVGGITET DATLAAASNA ILVGFNVRAD ASARKVIEAE SLDLRYYSVI YNLIDEVKAA MSGMLSPELK QQIIGLAEV RDVFKSPKFG AIAGCMVTEG VVKRHNPIRV LRDNVVIYEG ELESLRRFKD DVNEVRNGME CGIGVKNYND VRTGDVIEVF EIIEIQRTI A

UniProtKB: Translation initiation factor IF-2

+
Macromolecule #26: Translation initiation factor IF-3

MacromoleculeName: Translation initiation factor IF-3 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.600994 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKGGKRVQTA RPNRINGEIR AQEVRLTGLE GEQLGIVSLR EALEKAEEAG VDLVEISPNA EPPVCRIMDY GKFLYEKSKS SKEQKKKQK VIQVKEIKFR PGTDEGDYQV KLRSLIRFLE EGDKAKITLR FRGREMAHQQ IGMEVLNRVK DDLQELAVVE S FPTKIEGR QMIMVLAPKK KQ

UniProtKB: Translation initiation factor IF-3

+
Macromolecule #27: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 27 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

+
Macromolecule #28: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 28 / Number of copies: 152 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #29: (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2...

MacromoleculeName: (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4- ...Name: (2S,3S)-2-[[(2S)-2-[[(2S,4S)-5-aminocarbonyloxy-4-oxidanyl-2-[[(2S,3R)-3-oxidanylpiperidin-2-yl]carbonylamino]pentanoyl]amino]-3-(1H-imidazol-4-yl)propanoyl]amino]-3-(2-chloranyl-1H-imidazol-4-yl)-3-oxidanyl-propanoic acid
type: ligand / ID: 29 / Number of copies: 1 / Formula: A1IC4
Molecular weightTheoretical: 644.034 Da

+
Macromolecule #30: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 30 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.7
GridModel: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 232679
CTF correctionSoftware: (Name: CTFFIND, RELION) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 46163
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4ybb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9h9h:
Complex 1 30S-IF1-IF2-IF3-GE81112

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