[English] 日本語
Yorodumi
- PDB-3wbk: crystal structure analysis of eukaryotic translation initiation f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wbk
Titlecrystal structure analysis of eukaryotic translation initiation factor 5B and 1A complex
Components
  • Eukaryotic translation initiation factor 1A
  • Eukaryotic translation initiation factor 5B
KeywordsBIOSYNTHETIC PROTEIN / flexible / eukaryotic translation initiation
Function / homology
Function and homology information


formation of translation initiation ternary complex / translation reinitiation / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / protein-synthesizing GTPase / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...formation of translation initiation ternary complex / translation reinitiation / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / protein-synthesizing GTPase / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / translation initiation factor binding / translation initiation factor activity / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / translational initiation / cytoplasmic stress granule / double-stranded RNA binding / ribosome binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / GTPase activity / protein kinase binding / GTP binding / mitochondrion / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / eukaryotic translation initiation factor 1A ...Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 1A / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZheng, A. / Yamamoto, R. / Ose, T. / Yu, J. / Tanaka, I. / Yao, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: X-ray structures of eIF5B and the eIF5B-eIF1A complex: the conformational flexibility of eIF5B is restricted on the ribosome by interaction with eIF1A
Authors: Zheng, A. / Yu, J. / Yamamoto, R. / Ose, T. / Tanaka, I. / Yao, M.
History
DepositionMay 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5B
B: Eukaryotic translation initiation factor 5B
C: Eukaryotic translation initiation factor 1A


Theoretical massNumber of molelcules
Total (without water)150,4883
Polymers150,4883
Non-polymers00
Water00
1
A: Eukaryotic translation initiation factor 5B
C: Eukaryotic translation initiation factor 1A


Theoretical massNumber of molelcules
Total (without water)82,7642
Polymers82,7642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-5 kcal/mol
Surface area31350 Å2
MethodPISA
2
B: Eukaryotic translation initiation factor 5B


Theoretical massNumber of molelcules
Total (without water)67,7241
Polymers67,7241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.939, 120.942, 132.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 602 / Label seq-ID: 6 - 606

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Eukaryotic translation initiation factor 5B / eIF-5B / Translation initiation factor IF-2


Mass: 67724.023 Da / Num. of mol.: 2 / Fragment: UNP residues 401-1002
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: FUN12, YAL035W / Production host: Escherichia coli (E. coli) / Strain (production host): B834-CodonPlus(DE3)-RIL / References: UniProt: P39730
#2: Protein Eukaryotic translation initiation factor 1A / eIF-1A / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 15040.341 Da / Num. of mol.: 1 / Fragment: UNP residues 27-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TIF11, YMR260C, YM8156.02C / Production host: Escherichia coli (E. coli) / Strain (production host): B834-CodonPlus(DE3)-RIL / References: UniProt: P38912
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.76 % / Mosaicity: 0.422 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 100mM Tris-HCl pH 8.2, 12.5%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.98 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 24875 / % possible obs: 98.5 % / Observed criterion σ(I): -1.15 / Redundancy: 9.4 % / Rmerge(I) obs: 0.071 / Χ2: 1.371 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.425.80.49223180.753192.9
3.42-3.557.20.4124410.787198.6
3.55-3.728.80.32524600.826199.8
3.72-3.919.80.24925150.8221100
3.91-4.16100.14624870.8691100
4.16-4.4810.30.08424960.9891100
4.48-4.9310.60.06325191.141100
4.93-5.6410.60.07325351.451100
5.64-7.110.60.06525591.8011100
7.1-509.70.03325453.689194.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WBI

3wbi


Resolution: 3.3→40 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.3272 / WRfactor Rwork: 0.2706 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7357 / SU B: 36.687 / SU ML: 0.608 / SU Rfree: 0.6868 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.687 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3173 1769 7.1 %RANDOM
Rwork0.257 ---
obs0.2613 24828 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 349.8 Å2 / Biso mean: 159.3338 Å2 / Biso min: 47.82 Å2
Baniso -1Baniso -2Baniso -3
1--12.35 Å20 Å2-0 Å2
2--1.66 Å20 Å2
3---10.7 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9309 0 0 0 9309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199448
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.98512772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02651184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68924.988401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.218151780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7631555
X-RAY DIFFRACTIONr_chiral_restr0.0810.21510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216882
X-RAY DIFFRACTIONr_mcbond_it10.38315.6724757
X-RAY DIFFRACTIONr_mcangle_it16.55523.495934
X-RAY DIFFRACTIONr_scbond_it11.41816.0854691
Refine LS restraints NCS

Ens-ID: 1 / Number: 626 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.23 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.304→3.389 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 146 -
Rwork0.354 1504 -
all-1650 -
obs--89.77 %

+
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