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

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Basic information

Entry
Database: PDB / ID: 5me0
TitleStructure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112
Descriptor(30S ribosomal protein ...) x 20
(Translation initiation factor IF- ...) x 3
KeywordsRIBOSOME / Ribosome / Initiation of Translation
Specimen sourceThermus thermophilus (strain hb8 / atcc 27634 / dsm 579) / bacteria / thermophilic
Escherichia coli k-12 / bacteria / image: Escherichia coli
Geobacillus stearothermophilus / bacteria / thermophilic / ゲオバチルス・ステアロサーモフィルス
MethodElectron microscopy (13.5 Å resolution / Particle / Single particle)
AuthorsLopez-Alonso, J.P. / Fabbretti, A. / Kaminishi, T. / Iturrioz, I. / Brandi, L. / Gil Carton, D. / Gualerzi, C. / Fucini, P. / Connell, S.
CitationNucleic Acids Res., 2017, 45, 2179-2187

Nucleic Acids Res., 2017, 45, 2179-2187 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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2016 / Release: Jan 11, 2017
RevisionDateData content typeGroupProviderType
1.0Jan 11, 2017Structure modelrepositoryInitial release
1.1May 3, 2017Structure modelDatabase references

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein S21
V: Translation initiation factor IF-1
W: Translation initiation factor IF-2
Y: Translation initiation factor IF-3
Z: Translation initiation factor IF-3
X: fMet-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)953,58827
Polyers953,41026
Non-polymers1771
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules AX

#1: RNA chain16S ribosomal RNA


Mass: 497404.969 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: GenBank: 817573384
#26: RNA chainfMet-tRNA


Mass: 24818.893 Da / Num. of mol.: 1 / Details: Taken from PDB entry 3JCN / Source: (natural) Escherichia coli K-12 / References: GenBank: 731469900

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30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJK...

#2: Polypeptide(L)30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7V0

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7V3

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7V8

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7W1

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S6


Mass: 15211.058 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P02358

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein S7


Mass: 17637.445 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P02359

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7W7

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7X3

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#10: Polypeptide(L)30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7R5

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7R9

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#12: Polypeptide(L)30S ribosomal protein S12


Mass: 13683.053 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7S3

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7S9

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG59

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0ADZ4

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)30S ribosomal protein S16


Mass: 11464.126 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: A0A0U4BH30

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0AG63

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7T7

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7U3

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P0A7U7

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 / References: UniProt: P68679

Cellular component

Molecular function

Biological process

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Translation initiation factor IF- ... , 4 types, 4 molecules VWYZ

#22: Polypeptide(L)Translation initiation factor IF-1


Mass: 8247.664 Da / Num. of mol.: 1 / Details: Taken from PDB entry 1HR0
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
References: UniProt: Q5SHR1

Cellular component

Molecular function

#23: Polypeptide(L)Translation initiation factor IF-2


Mass: 97498.164 Da / Num. of mol.: 1 / Details: Taken from PDB entry 3JCN / Source: (gene. exp.) Escherichia coli K-12 / References: UniProt: P0A705

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)Translation initiation factor IF-3


Mass: 19717.984 Da / Num. of mol.: 1 / Details: Taken from PDB entry 1TIF / Source: (gene. exp.) Geobacillus stearothermophilus / References: UniProt: P03000

Cellular component

Molecular function

#25: Polypeptide(L)Translation initiation factor IF-3


Mass: 16667.477 Da / Num. of mol.: 1 / Details: Taken from PDB entry 2IFE / Source: (gene. exp.) Escherichia coli K-12 / References: UniProt: P0A707

Cellular component

Molecular function

Biological process

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Non-polymers , 1 types, 1 molecules

#27: ChemicalChemComp-FME / N-FORMYLMETHIONINE


Mass: 177.221 Da / Num. of mol.: 1 / Formula: C6H11NO3S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: 30S Pre-Initiation Complex Stalled by GE81112 / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26
Source: MULTIPLE SOURCES
Molecular weightExperimental flag: NO
Source (natural)Organism: Escherichia coli
Buffer solutionpH: 7.7
Buffer component
IDConc.Conc. unitsNameFormulaBuffer ID
110mMTrisTrisHCl1
27mMMagnesium chlorideMgCl21
360mMAmmonium acetateCH3CO2NH41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 2200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 74183 / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingAverage exposure time: 0.3 sec. / Electron dose: 17 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number of grids imaged: 1 / Number of real images: 261
EM imaging opticsEnergyfilter name: Omega
Image scansDimension width: 4096 / Dimension height: 4096

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting IDDetails
1Relion1.4PARTICLE SELECTION1
2DigitalMicrograph (GATAN)IMAGE ACQUISITION1
4CtfFind4CTF CORRECTION1
7SITUSMODEL FITTING1
9Relion1.4INITIAL EULER ASSIGNMENT1
10Relion1.4FINAL EULER ASSIGNMENT1
11Relion1.4CLASSIFICATION1
12Relion1.4RECONSTRUCTION1
13COOT0.8.3MODEL REFINEMENT1For minimizing the conformation of the linking residues of ligands that were fitted as multiple independent bodies i.e. domains G2-C1 and C2 of IF2, and residues 1-72 and 73-76 of the mRNA.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 174142
SymmetryPoint symmetry: C1
3D reconstructionResolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 23112 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingDetails: 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.
Ref protocol: RIGID BODY FIT
Atomic model building
IDPDB-IDPdb chain ID 3D fitting IDPdb chain residue range
14YBB1
23JCNv1
33JCNb1
41HR0W1
52IFEA190-180
61TIFA13-78

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