[English] 日本語
Yorodumi
- PDB-6kne: The C-terminal Domain of Translation Initiation Factor 5 at high pH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kne
TitleThe C-terminal Domain of Translation Initiation Factor 5 at high pH
ComponentsTranslation initiation factor eIF5
KeywordsTRANSLATION / Initiation Factor
Function / homology
Function and homology information


eukaryotic initiation factor eIF2 binding / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 48S preinitiation complex / GDP-dissociation inhibitor activity / negative regulation of translational initiation / translation initiation factor activity / GTPase activator activity / cytosolic ribosome assembly / GTP binding / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Translation initiation factor eIF5
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.701 Å
AuthorsJian, Y. / YuXin, Y. / Min, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17H05424 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: The pH-dependent conformational change of eukaryotic translation initiation factor 5: Insights into partner-binding manner.
Authors: Ye, Y. / Chen, M. / Kato, K. / Yao, M.
History
DepositionAug 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Translation initiation factor eIF5


Theoretical massNumber of molelcules
Total (without water)19,3771
Polymers19,3771
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9340 Å2
Unit cell
Length a, b, c (Å)49.950, 54.156, 63.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Translation initiation factor eIF5


Mass: 19376.928 Da / Num. of mol.: 1 / Fragment: C-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8PNF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: sodium citrate pH 5.5, 40% (v/v) PEG 600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→41.147 Å / Num. obs: 19254 / % possible obs: 99 % / Redundancy: 4.534 % / Biso Wilson estimate: 32.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.035 / Χ2: 1.055 / Net I/σ(I): 19.98 / Num. measured all: 87296
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.84.550.5082.7113958308930680.9710.57499.3
1.8-1.934.5160.2454.9912943290128660.9910.27898.8
1.93-2.084.6850.1438.1312659271227020.9960.16299.6
2.08-2.284.4380.07314.610998250524780.9980.08398.9
2.28-2.554.7160.04823.5510775229022850.9990.05499.8
2.55-2.944.4440.03532.748803202019810.9990.0498.1
2.94-3.64.6190.02944.637968173617250.9990.03399.4
3.6-5.074.3330.02650.235824137213440.9990.0398
5.07-41.1474.1840.02250.5433688268050.9990.02697.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.701→41.147 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 40.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 983 5.15 %
Rwork0.2301 18103 -
obs0.2319 19086 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.07 Å2 / Biso mean: 47.0899 Å2 / Biso min: 30.86 Å2
Refinement stepCycle: final / Resolution: 1.701→41.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1367 0 0 64 1431
Biso mean---49.47 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071394
X-RAY DIFFRACTIONf_angle_d0.9851879
X-RAY DIFFRACTIONf_chiral_restr0.037204
X-RAY DIFFRACTIONf_plane_restr0.005245
X-RAY DIFFRACTIONf_dihedral_angle_d15.462537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.701-1.79050.40741230.365253998
1.7905-1.90270.37671550.3143249397
1.9027-2.04960.40251410.3019253098
2.0496-2.25580.33381430.2656259799
2.2558-2.58220.31951440.2466258599
2.5822-3.25310.26681240.2494262898
3.2531-41.1470.22161530.1985273198

+
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