[English] 日本語
Yorodumi
- EMDB-3494: Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3494
TitleStructure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112
Map data
Sample
  • Complex: 30S Pre-Initiation Complex Stalled by GE81112
    • RNA: x 2 types
    • Protein or peptide: x 24 types
  • Ligand: x 1 types
KeywordsRibosome / Initiation of Translation
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 / ribosomal small subunit binding / RNA folding / chaperone-mediated protein folding / negative regulation of translational initiation ...ribosome disassembly / guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / ribosomal small subunit binding / RNA folding / chaperone-mediated protein folding / negative regulation of translational initiation / regulation of mRNA stability / response to cold / translation initiation factor activity / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / translational initiation / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / 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. / Ribosomal protein S14, bacterial/plastid / Elongation factor Tu domain 2 / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / 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 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 S2 signature 2. / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 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. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily
Similarity search - Domain/homology
30S ribosomal protein S16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-3 / Translation initiation factor IF-2 / 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 ...30S ribosomal protein S16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-3 / Translation initiation factor IF-2 / 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 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) / Escherichia coli K-12 (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Geobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.5 Å
AuthorsLopez-Alonso JP / Fabbretti A
Funding support Italy, Spain, 4 items
OrganizationGrant numberCountry
European UnionQLRT- 2001-00892 Italy
Marie Curie Actions; COFUND Spain
Marie Curie Action Career Integration GrantPCIG14-GA-2013-632072 Spain
Spanish Ministry of Economy and CompetitivenessCTQ2014-55907-R Spain
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.
Authors: Jorge P López-Alonso / Attilio Fabbretti / Tatsuya Kaminishi / Idoia Iturrioz / Letizia Brandi / David Gil-Carton / Claudio O Gualerzi / Paola Fucini / Sean R Connell /
Abstract: In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the ...In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.
History
DepositionNov 14, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseJan 11, 2017-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0747
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0747
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5me0
  • Surface level: 0.0747
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3494.png

Downloads & links

-
Map

FileDownload / File: emd_3494.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.02 Å/pix.
x 180 pix.
= 363.6 Å		2.02 Å/pix.
x 180 pix.
= 363.6 Å		2.02 Å/pix.
x 180 pix.
= 363.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0747 / Movie #1: 0.0747
Minimum - Maximum-0.083444044 - 0.34673113
Average (Standard dev.)0.005679719 (±0.031103546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 363.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.022.022.02
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z363.600363.600363.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0830.3470.006

-
Supplemental data

-
Mask #1

Fileemd_3494_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_3494_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_3494_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : 30S Pre-Initiation Complex Stalled by GE81112

EntireName: 30S Pre-Initiation Complex Stalled by GE81112
Components
  • Complex: 30S Pre-Initiation Complex Stalled by GE81112
    • 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: Translation initiation factor IF-1
    • Protein or peptide: Translation initiation factor IF-2
    • Protein or peptide: Translation initiation factor IF-3
    • Protein or peptide: Translation initiation factor IF-3
    • RNA: fMet-tRNA
  • Ligand: N-FORMYLMETHIONINE

+
Supramolecule #1: 30S Pre-Initiation Complex Stalled by GE81112

SupramoleculeName: 30S Pre-Initiation Complex Stalled by GE81112 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#26
Source (natural)Organism: Escherichia coli (E. coli)

+
Macromolecule #1: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 1 / Details: Taken from PDB entry 4YBB / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 497.404969 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 UCA

GENBANK: GENBANK: CP011320.1

+
Macromolecule #26: fMet-tRNA

MacromoleculeName: fMet-tRNA / type: rna / ID: 26 / Details: Taken from PDB entry 3JCN / Number of copies: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 24.818893 KDa
SequenceString:
CGCGGGG(4SU)GG AGCAGCCUGG (H2U)AGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGG(5MU)(PSU)CAAA UCCG GCCCC CGCAACCA

GENBANK: GENBANK: CP009789.1

+
Macromolecule #2: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 2 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 26.78167 KDa
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

+
Macromolecule #3: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 3 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 26.031316 KDa
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

+
Macromolecule #4: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 4 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 23.514199 KDa
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

+
Macromolecule #5: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 5 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 17.629398 KDa
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

+
Macromolecule #6: 30S ribosomal protein S6

MacromoleculeName: 30S ribosomal protein S6 / type: protein_or_peptide / ID: 6 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 15.211058 KDa
SequenceString:
MRHYEIVFMV HPDQSEQVPG MIERYTAAIT GAEGKIHRLE DWGRRQLAYP INKLHKAHYV LMNVEAPQEV IDELETTFRF NDAVIRSMV MRTKHAVTEA SPMVKAKDER RERRDDFANE TADDAEAGDS EE

UniProtKB: Small ribosomal subunit protein bS6

+
Macromolecule #7: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 7 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 17.637445 KDa
SequenceString:
MPRRRVIGQR KILPDPKFGS ELLAKFVNIL MVDGKKSTAE SIVYSALETL AQRSGKSELE AFEVALENVR PTVEVKSRRV GGSTYQVPV EVRPVRRNAL AMRWIVEAAR KRGDKSMALR LANELSDAAE NKGTAVKKRE DVHRMAEANK AFAHYRW

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #8: 30S ribosomal protein S8

MacromoleculeName: 30S ribosomal protein S8 / type: protein_or_peptide / ID: 8 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 14.146557 KDa
SequenceString:
MSMQDPIADM LTRIRNGQAA NKAAVTMPSS KLKVAIANVL KEEGFIEDFK VEGDTKPELE LTLKYFQGKA VVESIQRVSR PGLRIYKRK DELPKVMAGL GIAVVSTSKG VMTDRAARQA GLGGEIICYV A

UniProtKB: Small ribosomal subunit protein uS8

+
Macromolecule #9: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 9 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 14.88627 KDa
SequenceString:
MAENQYYGTG RRKSSAARVF IKPGNGKIVI NQRSLEQYFG RETARMVVRQ PLELVDMVEK LDLYITVKGG GISGQAGAIR HGITRALME YDESLRSELR KAGFVTRDAR QVERKKVGLR KARRRPQFSK R

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #10: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 10 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.755597 KDa
SequenceString:
MQNQRIRIRL KAFDHRLIDQ ATAEIVETAK RTGAQVRGPI PLPTRKERFT VLISPHVNKD ARDQYEIRTH LRLVDIVEPT EKTVDALMR LDLAAGVDVQ ISLG

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #11: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 11 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 13.870975 KDa
SequenceString:
MAKAPIRARK RVRKQVSDGV AHIHASFNNT IVTITDRQGN ALGWATAGGS GFRGSRKSTP FAAQVAAERC ADAVKEYGIK NLEVMVKGP GPGRESTIRA LNAAGFRITN ITDVTPIPHN GCRPPKKRRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #12: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 12 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 13.683053 KDa
SequenceString:
ATVNQLVRKP RARKVAKSNV PALEACPQKR GVCTRVYTTT PKKPNSALRK VCRVRLTNGF EVTSYIGGEG HNLQEHSVIL IRGGRVK(D2T)L PGVRYHTVRG ALDCSGVKDR KQARSKYGVK RPKA

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #13: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 13 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 13.128467 KDa
SequenceString:
MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGL RHRRGLPVRG QRTKTNARTR KGPRKPIKK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #14: 30S ribosomal protein S14

MacromoleculeName: 30S ribosomal protein S14 / type: protein_or_peptide / ID: 14 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.60656 KDa
SequenceString:
MAKQSMKARE VKRVALADKY FAKRAELKAI ISDVNASDED RWNAVLKLQT LPRDSSPSRQ RNRCRQTGRP HGFLRKFGLS RIKVREAAM RGEIPGLKKA SW

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #15: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 15 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 10.290816 KDa
SequenceString:
MSLSTEATAK IVSEFGRDAN DTGSTEVQVA LLTAQINHLQ GHFAEHKKDH HSRRGLLRMV SQRRKLLDYL KRKDVARYTQ LIERLGLRR

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #16: 30S ribosomal protein S16

MacromoleculeName: 30S ribosomal protein S16 / type: protein_or_peptide / ID: 16 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.464126 KDa
SequenceString:
MTPDSVPRWG PVVLFTQEDV MVTIRLARHG AKKRPFYQVV VADSRNARNG RFIERVGFFN PIASEKEEGT RLDLDRIAHW VGQGATISD RVAALIKEVN KAA

UniProtKB: 30S ribosomal protein S16

+
Macromolecule #17: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 17 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 9.724491 KDa
SequenceString:
MTDKIRTLQG RVVSDKMEKS IVVAIERFVK HPIYGKFIKR TTKLHVHDEN NECGIGDVVE IRECRPLSKT KSWTLVRVVE KAVL

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #18: 30S ribosomal protein S18

MacromoleculeName: 30S ribosomal protein S18 / type: protein_or_peptide / ID: 18 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 9.005472 KDa
SequenceString:
MARYFRRRKF CRFTAEGVQE IDYKDIATLK NYITESGKIV PSRITGTRAK YQRQLARAIK RARYLSLLPY TDRHQ

UniProtKB: Small ribosomal subunit protein bS18

+
Macromolecule #19: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 19 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 10.455355 KDa
SequenceString:
MPRSLKKGPF IDLHLLKKVE KAVESGDKKP LRTWSRRSTI FPNMIGLTIA VHNGRQHVPV FVTDEMVGHK LGEFAPTRTY RGHAADKKA KKK

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #20: 30S ribosomal protein S20

MacromoleculeName: 30S ribosomal protein S20 / type: protein_or_peptide / ID: 20 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 9.708464 KDa
SequenceString:
MANIKSAKKR AIQSEKARKH NASRRSMMRT FIKKVYAAIE AGDKAAAQKA FNEMQPIVDR QAAKGLIHKN KAARHKANLT AQINKLA

UniProtKB: Small ribosomal subunit protein bS20

+
Macromolecule #21: 30S ribosomal protein S21

MacromoleculeName: 30S ribosomal protein S21 / type: protein_or_peptide / ID: 21 / Details: Taken from PDB entry 4YBB / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 8.524039 KDa
SequenceString:
MPVIKVRENE PFDVALRRFK RSCEKAGVLA EVRRREFYEK PTTERKRAKA SAVKRHAKKL ARENARRTRL Y

UniProtKB: Small ribosomal subunit protein bS21

+
Macromolecule #22: Translation initiation factor IF-1

MacromoleculeName: Translation initiation factor IF-1 / type: protein_or_peptide / ID: 22 / Details: Taken from PDB entry 1HR0 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
Molecular weightTheoretical: 8.247664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKEKDTIRT EGVVTEALPN ATFRVKLDSG PEILAYISGK MRMHYIRILP GDRVVVEITP YDPTRGRIVY RK

UniProtKB: Translation initiation factor IF-1

+
Macromolecule #23: Translation initiation factor IF-2

MacromoleculeName: Translation initiation factor IF-2 / type: protein_or_peptide / ID: 23 / Details: Taken from PDB entry 3JCN / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
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 #24: Translation initiation factor IF-3

MacromoleculeName: Translation initiation factor IF-3 / type: protein_or_peptide / ID: 24 / Details: Taken from PDB entry 1TIF / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 19.717984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SKDFIINEQI RAREVRLIDQ NGDQLGIKSK QEALEIAARR NLDLVLVAPN AKPPVCRIMD YGKFRFEQQK KEKEARKKQK VINVKEVRL SPTIEEHDFN TKLRNARKFL EKGDKVKATI RFKGRAITHK EIGQRVLDRL SEACADIAVV ETAPKMDGRN M FLVLAPKN DNK

UniProtKB: Translation initiation factor IF-3

+
Macromolecule #25: Translation initiation factor IF-3

MacromoleculeName: Translation initiation factor IF-3 / type: protein_or_peptide / ID: 25 / Details: Taken from PDB entry 2IFE / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 16.667477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSLREALEKA EEAGVDLVEI SPNAEPPVCR IMDYGKFLYE KSKSSKEQKK KQKVIQVKEI KFRPGTDEGD YQVKLRSLIR FLEEGDKAK ITLRFRGREM AHQQIGMEVL NRVKDDLQEL AVVESFPTKI EGRQMIMVLA PKKKQ

UniProtKB: Translation initiation factor IF-3

+
Macromolecule #27: N-FORMYLMETHIONINE

MacromoleculeName: N-FORMYLMETHIONINE / type: ligand / ID: 27 / Number of copies: 1 / Formula: FME
Molecular weightTheoretical: 177.221 Da
Chemical component information

ChemComp-FME:
N-FORMYLMETHIONINE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.7
Component:
ConcentrationFormulaName
10.0 mMTrisHClTris
7.0 mMMgCl2Magnesium chloride
60.0 mMCH3CO2NH4Ammonium acetate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeJEOL 2200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 261 / Average exposure time: 0.3 sec. / Average electron dose: 17.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 74183 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 174142
Startup modelType of model: OTHER / Details: Previous empty 30S volume obtained in our lab.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 23112
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

4ybb

source_name: PDB, initial_model_type: experimental model

3jcn

chain_id: v, source_name: PDB, initial_model_type: experimental model

3jcn

chain_id: b, source_name: PDB, initial_model_type: experimental model

1hr0

chain_id: W, source_name: PDB, initial_model_type: experimental model

2ife

chain_id: A, residue_range: 90-180, source_name: PDB, initial_model_type: experimental model

1tif

chain_id: A, residue_range: 3-78, source_name: PDB, initial_model_type: experimental model
DetailsThe fitting of the model to the EM volume was performed through rigid body fitting. The head and the body of the 30S were treated as independent bodies. Due to the low resolution of the volume, the conformation of the linking bases was not minimized. In addition, some of the clashes of the model are produced by flexible loops or protein side chains that were not refined.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-5me0:
Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112

+
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