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- EMDB-3494: Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled ... -

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Basic information

Entry
Database: EMDB / ID: 3494
TitleStructure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112
Sample30S Pre-Initiation Complex Stalled by GE81112
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Escherichia coli k-12 / bacteria / image: Escherichia coli
Map data
Methodsingle particle reconstruction, at 13.5 A resolution
AuthorsLopez-Alonso JP / Fabbretti A
CitationNucleic Acids Res., 2016

Nucleic Acids Res., 2016 StrPapers
Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.
Jorge P López-Alonso / Attilio Fabbretti / Tatsuya Kaminishi / Idoia Iturrioz / Letizia Brandi / David Gil-Carton / Claudio O Gualerzi / Paola Fucini / Sean R Connell

DateDeposition: Nov 14, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Jan 11, 2017 / Last update: Nov 14, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0747
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.0747
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5me0
  • Surface level: 0.0747
  • Imaged by UCSF CHIMERA
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Map

Fileemd_3494.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
2.02 A/pix
= 363.6 A
180 pix
2.02 A/pix
= 363.6 A
180 pix
2.02 A/pix
= 363.6 A

Surface

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.02 A
Density
Contour Level:0.0747 (by author), 0.0747 (movie #1):
Minimum - Maximum-0.083444044 - 0.34673113
Average (Standard dev.)0.005679719 (0.031103546)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin000
Limit179179179
Spacing180180180
CellA=B=C: 363.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0830.3470.006

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Supplemental data

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Mask #1

Fileemd_3494_msk_1.map ( map file in CCP4 format, 23329 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3494_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire 30S Pre-Initiation Complex Stalled by GE81112

EntireName: 30S Pre-Initiation Complex Stalled by GE81112 / Number of components: 28

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Component #1: protein, 30S Pre-Initiation Complex Stalled by GE81112

ProteinName: 30S Pre-Initiation Complex Stalled by GE81112 / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Details: Taken from PDB entry 4YBB / Structure: OTHER / Synthetic: No
Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU AAUACCGCAU AACGUCGCAA GACCAAAGAG GGGGACCUUC GGGCCUCUUG CCAUCGGAUG UGCCCAGAUG GGAUUAGCUA GUAGGUGGGG UAACGGCUCA CCUAGGCGAC GAUCCCUAGC UGGUCUGAGA GGAUGACCAG CCACACUGGA ACUGAGACAC GGUCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGAAGGCCU UCGGGUUGUA AAGUACUUUC AGCGGGGAGG AAGGGAGUAA AGUUAAUACC UUUGCUCAUU GACGUUACCC GCAGAAGAAG CACCGGCUAA CUCCG(PSU)GCCA GCAGCC(G7M)CGG UAAUACGGAG GGUGCAAGCG UUAAUCGGAA UUACUGGGCG UAAAGCGCAC GCAGGCGGUU UGUUAAGUCA GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCUGA UACUGGCAAG CUUGAGUCUC GUAGAGGGGG GUAGAAUUCC AGGUGUAGCG GUGAAAUGCG UAGAGAUCUG GAGGAAUACC GGUGGCGAAG GCGGCCCCCU GGACGAAGAC UGACGCUCAG GUGCGAAAGC GUGGGGAGCA AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAU(2MG)(5MC)AAC GCGAAGAACC UUACCUGGUC UUGACAUCCA CGGAAGUUUU CAGAGAUGAG AAUGUGCCUU CGGGAACCGU GAGACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUUGUGA AAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUAUCC UUUGUUGCCA GCGGUCCGGC CGGGAACUCA AAGGAGACUG CCAGUGAUAA ACUGGAGGAA GGUGGGGAUG ACGUCAAGUC AUCAUG(2MG)CCC UUACGACCAG GGCUACACAC GUGCUACAAU GGCGCAUACA AAGAGAAGCG ACCUCGCGAG AGCAAGCGGA CCUCAUAAAG UGCGUCGUAG UCCGGAUUGG AGUCUGCAAC UCGACUCCAU GAAGUCGGAA UCGCUAGUAA UCGUGGAUCA GAAUGCCACG GUGAAUACGU UCCCGGGCCU UGUACACACC G(4OC)CCGU(5MC)ACA CCAUGGGAGU GGGUUGCAAA AGAAGUAGGU AGCUUAACCU UCGGGAGGGC GCUUACCACU UUGUGAUUCA UGACUGGGGU GAAGUCG(UR3)AA CAAGGUAACC GUAGG(2MG)G(MA6)(MA6)C CUGCGGUUGG AUCA
MassTheoretical: 497.404969 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #5: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #6: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #7: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 15.211058 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #8: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 17.637445 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #9: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #10: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #11: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #12: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #13: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 13.683053 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #14: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #15: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #16: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 10.290816 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #17: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 11.464126 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #18: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #19: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #20: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #21: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #22: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Details: Taken from PDB entry 4YBB / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #23: protein, Translation initiation factor IF-1

ProteinName: Translation initiation factor IF-1 / Details: Taken from PDB entry 1HR0 / Recombinant expression: No
MassTheoretical: 8.247664 kDa
Source (engineered)Expression System: Thermus thermophilus (strain hb8 / atcc 27634 / dsm 579) / bacteria / thermophilic
Strain: HB8 / ATCC 27634 / DSM 579

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Component #24: protein, Translation initiation factor IF-2

ProteinName: Translation initiation factor IF-2 / Details: Taken from PDB entry 3JCN / Recombinant expression: No
MassTheoretical: 97.498164 kDa
Source (engineered)Expression System: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #25: protein, Translation initiation factor IF-3

ProteinName: Translation initiation factor IF-3 / Details: Taken from PDB entry 1TIF / Recombinant expression: No
MassTheoretical: 19.717984 kDa
Source (engineered)Expression System: Geobacillus stearothermophilus / bacteria / thermophilic / ゲオバチルス・ステアロサーモフィルス

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Component #26: protein, Translation initiation factor IF-3

ProteinName: Translation initiation factor IF-3 / Details: Taken from PDB entry 2IFE / Recombinant expression: No
MassTheoretical: 16.667477 kDa
Source (engineered)Expression System: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #27: nucleic-acid, fMet-tRNA

Nucleic-acidName: fMet-tRNA / Class: RNA / Details: Taken from PDB entry 3JCN / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGG(4SU)GG AGCAGCCUGG (H2U)AGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGG(5MU)(PSU)CAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.818893 kDa
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #28: ligand, N-FORMYLMETHIONINE

LigandName: N-FORMYLMETHIONINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.177221 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.7
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 95 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 74183 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: Omega
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 261

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 23112
3D reconstructionSoftware: Relion / Resolution: 13.5 A / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Details: The 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.
Input PDB model: 4YBB, 3JCN, 3JCN, 1HR0, 2IFE, 1TIF
Chain ID: 3JCN_v, 3JCN_b, 1HR0_W, 2IFE_A, 1TIF_A
Output model

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