[English] 日本語
Yorodumi
- PDB-9v5s: Crystal structure of EF-Tu from Mycoplasma pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v5s
TitleCrystal structure of EF-Tu from Mycoplasma pneumoniae
ComponentsElongation factor Tu
KeywordsBIOSYNTHETIC PROTEIN / Mycoplasma pneumoniae / EF-Tu
Function / homology
Function and homology information


protein-synthesizing GTPase / fibronectin binding / translation elongation factor activity / external side of plasma membrane / GTPase activity / GTP binding / membrane / cytosol
Similarity search - Function
Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / 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 ...Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / 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. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsLiu, Y.H. / Wang, W.M. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118 China
CitationJournal: J.Mol.Struct. / Year: 2026
Title: Structural insights of the first elongation factor EF-Tu complexes from mycoplasma
Authors: Liu, Y.H. / Ma, D. / Yao, H. / Gong, W. / Xie, L. / Zhao, Y. / Zhao, Y. / Wang, W.M. / Wang, H.F.
History
DepositionMay 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongation factor Tu
B: Elongation factor Tu
C: Elongation factor Tu
D: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,71912
Polymers172,8494
Non-polymers1,8708
Water11,656647
1
A: Elongation factor Tu
B: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3606
Polymers86,4252
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-44 kcal/mol
Surface area32560 Å2
MethodPISA
2
C: Elongation factor Tu
hetero molecules

D: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3606
Polymers86,4252
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y+1/2,-z+3/21
Buried area3800 Å2
ΔGint-47 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.382, 106.733, 257.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Elongation factor Tu / EF-Tu


Mass: 43212.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1) (bacteria)
Gene: tuf, MPN_665, MP177 / Production host: Escherichia coli (E. coli) / References: UniProt: P23568, protein-synthesizing GTPase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Ammonium tartrate dibasic, PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.24→128.8 Å / Num. obs: 86227 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.047 / Rrim(I) all: 0.16 / Χ2: 0.98 / Net I/σ(I): 13.9 / Num. measured all: 1003354
Reflection shellResolution: 2.24→2.36 Å / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 1.115 / Num. measured all: 129703 / Num. unique obs: 12435 / CC1/2: 0.709 / Rpim(I) all: 0.361 / Rrim(I) all: 1.173 / Χ2: 0.88 / Net I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→23.2 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1998 2.32 %
Rwork0.2036 --
obs0.2045 86029 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11700 0 116 647 12463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212014
X-RAY DIFFRACTIONf_angle_d0.56116267
X-RAY DIFFRACTIONf_dihedral_angle_d7.9251688
X-RAY DIFFRACTIONf_chiral_restr0.0441869
X-RAY DIFFRACTIONf_plane_restr0.0042090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.31931420.27295968X-RAY DIFFRACTION100
2.3-2.360.26361390.26045888X-RAY DIFFRACTION100
2.36-2.430.34121420.25065947X-RAY DIFFRACTION100
2.43-2.510.30591410.24235906X-RAY DIFFRACTION100
2.51-2.60.2681410.23275973X-RAY DIFFRACTION100
2.6-2.70.26091420.23075913X-RAY DIFFRACTION100
2.7-2.820.30711420.23465979X-RAY DIFFRACTION100
2.82-2.970.29281410.23635965X-RAY DIFFRACTION100
2.97-3.160.32191410.23115946X-RAY DIFFRACTION100
3.16-3.40.23351440.21316009X-RAY DIFFRACTION100
3.4-3.740.21811420.19456022X-RAY DIFFRACTION100
3.74-4.280.22331450.17216078X-RAY DIFFRACTION100
4.28-5.380.19081450.16376105X-RAY DIFFRACTION100
5.38-23.20.1911510.18116332X-RAY DIFFRACTION100

+
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