[English] 日本語
Yorodumi
- PDB-7csl: Crystal structure of the archaeal EF1A-EF1B complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7csl
TitleCrystal structure of the archaeal EF1A-EF1B complex
Components
  • Elongation factor 1-alpha
  • Elongation factor 1-beta
KeywordsTRANSLATION / translation elongation / Guanine exchange
Function / homology
Function and homology information


sulfur compound metabolic process / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EF1B, beta chain, archaeal / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain / EF-1 guanine nucleotide exchange domain / Translation elongation factor EF1A, eukaryotic/archaeal / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site ...Translation elongation factor EF1B, beta chain, archaeal / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain / EF-1 guanine nucleotide exchange domain / Translation elongation factor EF1A, eukaryotic/archaeal / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation elongation factor EF1B/ribosomal protein S6 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongation factor 1-alpha / Elongation factor 1-beta
Similarity search - Component
Biological speciesPyrococcus horikoshii OT-3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSuzuki, T. / Ito, K. / Miyoshi, T. / Murakami, R. / Uchiumi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H03155 Japan
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural insights into the Switching Off of the Interaction between the Archaeal Ribosomal Stalk and aEF1A by Nucleotide Exchange Factor aEF1B.
Authors: Suzuki, T. / Ito, K. / Miyoshi, T. / Murakami, R. / Uchiumi, T.
History
DepositionAug 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongation factor 1-alpha
B: Elongation factor 1-alpha
C: Elongation factor 1-beta
D: Elongation factor 1-beta


Theoretical massNumber of molelcules
Total (without water)117,5804
Polymers117,5804
Non-polymers00
Water4,522251
1
A: Elongation factor 1-alpha
C: Elongation factor 1-beta


Theoretical massNumber of molelcules
Total (without water)58,7902
Polymers58,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-15 kcal/mol
Surface area21640 Å2
MethodPISA
2
B: Elongation factor 1-alpha
D: Elongation factor 1-beta


Theoretical massNumber of molelcules
Total (without water)58,7902
Polymers58,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-14 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.149, 70.194, 77.822
Angle α, β, γ (deg.)112.900, 91.770, 89.980
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Elongation factor 1-alpha / EF-1-alpha / Elongation factor Tu / EF-Tu


Mass: 48426.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT-3 (archaea) / Strain: OT-3 / Gene: tuf, PH1484, PHCC033 / Production host: Escherichia coli (E. coli) / References: UniProt: O59153
#2: Protein Elongation factor 1-beta / EF-1-beta / aEF-1beta


Mass: 10363.706 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT-3 (archaea) / Strain: OT-3 / Gene: ef1b, PH0026.1 / Production host: Escherichia coli (E. coli) / References: UniProt: P58748
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES-NaOH pH 7.0, 10% w/v PEG6000, 5% v/v MPD

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.891
11h,-k,-l20.109
ReflectionResolution: 2→44.41 Å / Num. obs: 70518 / % possible obs: 96.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.12 Å / Rmerge(I) obs: 0.32 / Num. unique obs: 10918

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WY9, 2YY3

3wy9

2yy3


Resolution: 2→44.41 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.055 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 3475 5 %RANDOM
Rwork0.2247 ---
obs0.2273 66026 95.18 %-
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: 94.63 Å2 / Biso mean: 49.397 Å2 / Biso min: 27.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0.16 Å2-0.63 Å2
2---2.78 Å20.55 Å2
3---1.03 Å2
Refinement stepCycle: final / Resolution: 2→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7992 0 0 251 8243
Biso mean---49.87 -
Num. residues----1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198158
X-RAY DIFFRACTIONr_bond_other_d0.0020.028124
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.97211046
X-RAY DIFFRACTIONr_angle_other_deg1.007318780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25251012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49424.709344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.771151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0971542
X-RAY DIFFRACTIONr_chiral_restr0.1010.21266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218996
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021682
LS refinement shellResolution: 2→2.048 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 230 -
Rwork0.296 4384 -
obs--85.13 %

+
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