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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wbi
TitleCrystal structure analysis of eukaryotic translation initiation factor 5B structure I
ComponentsEukaryotic translation initiation factor 5B
KeywordsBIOSYNTHETIC PROTEIN / flexible / eukaryotic translation initiation / eIF1A
Function / homology
Function and homology information


protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translational initiation / translation initiation factor activity / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translational initiation / translation initiation factor activity / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / cytoplasmic stress granule / ribosome binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / GTPase activity / GTP binding / mitochondrion / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 ...Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 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 / 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 5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5B


Theoretical massNumber of molelcules
Total (without water)67,7241
Polymers67,7241
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.570, 129.570, 70.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-787-

HOH

21A-788-

HOH

-
Components

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


Mass: 67724.023 Da / Num. of mol.: 1 / 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 / Plasmid: pDBHT2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834-CodonPlus(DE3)-RIL / References: UniProt: P39730
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Tri-Sodium Citrate, 19% PEG 3350, HEPES pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2008
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→43.19 Å / Num. obs: 25590 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 54.799 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.35-2.490.5070.9973.1956684407139731.03497.6
2.49-2.660.3050.6385.0856136382738270.661100
2.66-2.870.1850.3898.1652366357335730.403100
2.87-3.140.0940.19415.4648206331233120.201100
3.14-3.510.0470.10226.9643301302230220.106100
3.51-4.050.0290.06539.2937107266626650.068100
4.05-4.950.0180.04553.1731027229722970.046100
4.95-6.950.0180.04452.523636181618160.046100
6.950.0110.03160.6613308112011050.03298.7

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
SHELXCDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→40.97 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2572 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8154 / SU B: 8.552 / SU ML: 0.205 / SU R Cruickshank DPI: 0.4946 / SU Rfree: 0.2869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.495 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1821 7.1 %RANDOM
Rwork0.2104 ---
obs0.2145 25589 99.56 %-
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: 167.45 Å2 / Biso mean: 53.8743 Å2 / Biso min: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 0 93 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194683
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9866329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5695586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95325.025199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7281527
X-RAY DIFFRACTIONr_chiral_restr0.070.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213406
X-RAY DIFFRACTIONr_mcbond_it3.1015.0562350
X-RAY DIFFRACTIONr_mcangle_it4.9247.5762934
X-RAY DIFFRACTIONr_scbond_it3.9385.6762329
LS refinement shellResolution: 2.346→2.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 130 -
Rwork0.272 1639 -
all-1769 -
obs--94.75 %

+
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://pdbjlvh1.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