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- PDB-7vmx: The Crystal Structure of EF-Tu and EF-Ts complex from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 7vmx
TitleThe Crystal Structure of EF-Tu and EF-Ts complex from Mycobacterium tuberculosis
Components
  • Elongation factor Ts
  • Elongation factor Tu
KeywordsElongation Factor / Mycobacterium tuberculosis / Protein translation / TRANSLATION
Function / homology
Function and homology information


protein-synthesizing GTPase / translation elongation factor activity / GTPase activity / GTP binding / magnesium ion binding / cytoplasm / cytosol
Similarity search - Function
Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / Ubiquitin-associated (UBA) domain / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle ...Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / Ubiquitin-associated (UBA) domain / 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 / UBA-like superfamily / 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 / Helicase, Ruva Protein; 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 nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Elongation factor Ts / Elongation factor Tu
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhan, B.W. / Li, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: Commun Biol / Year: 2022
Title: Structural insights of the elongation factor EF-Tu complexes in protein translation of Mycobacterium tuberculosis.
Authors: Zhan, B. / Gao, Y. / Gao, W. / Li, Y. / Li, Z. / Qi, Q. / Lan, X. / Shen, H. / Gan, J. / Zhao, G. / Li, J.
History
DepositionOct 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Ts
B: Elongation factor Tu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8619
Polymers72,4442
Non-polymers4177
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-102 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.114, 128.114, 200.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Elongation factor Ts / EF-Ts


Mass: 28794.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: tsf, C0094_15805, DSI38_05510, E5M05_16495, E5M52_15015, E5M78_14905, ERS007663_01361, ERS007665_01339, ERS007670_03302, ERS007688_01011, ERS013471_00410, ERS023446_00764, ERS024276_02208, ...Gene: tsf, C0094_15805, DSI38_05510, E5M05_16495, E5M52_15015, E5M78_14905, ERS007663_01361, ERS007665_01339, ERS007670_03302, ERS007688_01011, ERS013471_00410, ERS023446_00764, ERS024276_02208, ERS027646_02463, ERS027659_03596, ERS027661_01399, ERS094182_02070, F6W99_01501, GCL30_16350, SAMEA2683035_02109
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IDC3
#2: Protein Elongation factor Tu / EF-Tu


Mass: 43649.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: tuf_1, tuf, C0094_03695, DSI38_24795, E5M05_06550, E5M52_05390, E5M78_06185, ERS007657_00720, ERS007663_01319, ERS007670_02372, ERS007703_04298, ERS007720_00657, ERS007722_02966, ERS013471_ ...Gene: tuf_1, tuf, C0094_03695, DSI38_24795, E5M05_06550, E5M52_05390, E5M78_06185, ERS007657_00720, ERS007663_01319, ERS007670_02372, ERS007703_04298, ERS007720_00657, ERS007722_02966, ERS013471_00592, ERS023446_00428, ERS024276_01766, ERS027646_00039, ERS027659_02599, ERS027661_00652, ERS094182_01322, F6W99_03360, GCL30_03260, SAMEA2683035_02505
Production host: Escherichia coli (E. coli) / References: UniProt: A0A045IWT1
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.68 Å3/Da / Density % sol: 78.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM TRIS hydrochloride pH 9.0, 8% PEG 6000, 2mM Zinc chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: -l,-k,-h / Fraction: 0.07
ReflectionResolution: 2.8→30 Å / Num. obs: 41642 / % possible obs: 98.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.036 / Rrim(I) all: 0.145 / Χ2: 1.003 / Net I/σ(I): 5 / Num. measured all: 557995
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.96.20.53537630.250.1910.5730.73491.2
2.9-3.027.80.51640680.4460.1760.5480.73798.5
3.02-3.158.90.49841170.6330.1660.5260.77599.5
3.15-3.3211.70.45341460.8160.1290.4720.8699.9
3.32-3.5313.20.38341620.930.1030.3970.966100
3.53-3.814.60.28341900.9790.0720.2921.08499.9
3.8-4.1815.10.19341980.9920.0490.1991.16499.9
4.18-4.7818.90.11542310.9980.0260.1181.18100
4.78-6.0217.70.10642740.9980.0240.1081.11399.9
6.02-3018.40.06544930.9980.0150.0660.9199.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFC

1efc


Resolution: 2.8→29.86 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1818 4.96 %RANDOM
Rwork0.2316 34800 --
obs0.2334 36618 87.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.33 Å2 / Biso mean: 50.1884 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: final / Resolution: 2.8→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 7 4 4717
Biso mean--79.8 38.28 -
Num. residues----619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.880.4547500.353791396331
2.88-2.960.3591670.34431413148047
2.96-3.060.41181190.34042196231573
3.06-3.160.3411450.32792740288591
3.16-3.290.34671310.30732995312698
3.29-3.440.34111650.278529753140100
3.44-3.620.27581680.260330263194100
3.62-3.850.31431540.238830383192100
3.85-4.140.23911410.213830713212100
4.14-4.560.25161660.184730603226100
4.56-5.220.22141580.179330833241100
5.22-6.560.23521720.211631163288100
6.56-29.860.19521820.18383174335697

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