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- PDB-7vmc: Crystal structure of EF-Tu/CdiA/CdiI -

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Basic information

Entry
Database: PDB / ID: 7vmc
TitleCrystal structure of EF-Tu/CdiA/CdiI
Components
  • Contact-dependent inhibitor I
  • Elongation factor Tu
  • tRNA nuclease CdiA
KeywordsTOXIN / Contact-dependent growth inhibition / elongation factor
Function / homology
Function and homology information


guanosine tetraphosphate binding / translation elongation factor activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / GTPase activity / GTP binding / extracellular region / cytosol
Similarity search - Function
Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle ...Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity 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 / Pectin lyase fold / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Pectin lyase fold/virulence factor / 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
Uncharacterized protein / tRNA nuclease CdiA / Elongation factor Tu
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.413 Å
AuthorsWang, J. / Yashiro, Y. / Tomita, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26113002 Japan
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Mechanistic insights into tRNA cleavage by a contact-dependent growth inhibitor protein and translation factors.
Authors: Wang, J. / Yashiro, Y. / Sakaguchi, Y. / Suzuki, T. / Tomita, K.
History
DepositionOct 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Tu
B: tRNA nuclease CdiA
C: Contact-dependent inhibitor I


Theoretical massNumber of molelcules
Total (without water)96,5013
Polymers96,5013
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.930, 102.760, 88.140
Angle α, β, γ (deg.)90.000, 111.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Elongation factor Tu / EF-Tu


Mass: 44441.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2QJ06
#2: Protein tRNA nuclease CdiA / tRNase CdiA / CdiA-EC869 / Toxin CdiA


Mass: 32256.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (strain EC869) (bacteria)
Gene: cdiA1, ECH7EC869_5848 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3BM48, Hydrolases; Acting on ester bonds
#3: Protein Contact-dependent inhibitor I


Mass: 19802.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (strain EC869) (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A3ULE6

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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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 3350, 100mM HEPES-KOH pH7.5, 2% Tacsimate pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→35.603 Å / Num. obs: 11523 / % possible obs: 98.1 % / Redundancy: 7.486 % / Biso Wilson estimate: 109.04 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.308 / Rrim(I) all: 0.328 / Χ2: 0.753 / Net I/σ(I): 7.12 / Num. measured all: 86262 / Scaling rejects: 43
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
3.4-3.496.3212.4370.8545458487190.3242.63184.8
3.49-3.587.4651.7921.463908598560.4861.92199.7
3.58-3.697.7221.5041.7562018088030.6171.60699.4
3.69-3.87.9291.2122.363278057980.7271.29299.1
3.8-3.927.7991.1362.6859827697670.8591.21199.7
3.92-4.067.9780.9233.5558327397310.8980.98198.9
4.06-4.227.8060.6844.656447247230.940.72999.9
4.22-4.397.6730.5366.0653026966910.9670.57199.3
4.39-4.587.5820.3947.8848986506460.980.4299.4
4.58-4.817.3160.3479.0147486546490.9890.3799.2
4.81-5.076.9260.3279.3541005945920.9870.3599.7
5.07-5.377.0360.319.7540535795760.9910.33199.5
5.37-5.747.7440.3418.8141205415320.9870.36398.3
5.74-6.217.9980.2969.9840075075010.9930.31498.8
6.21-6.87.8830.24811.6436504694630.9920.26398.7
6.8-7.67.6870.18513.8631674144120.9940.19699.5
7.6-8.787.4010.11118.927683773740.9950.11999.2
8.78-10.756.5210.0821.1520413223130.9970.08697.2
10.75-15.27.1560.07323.5117392482430.9960.07898
15.2-35.6035.5820.07719.57481461340.9950.08491.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PC3

4pc3


Resolution: 3.413→35.603 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 571 5.01 %
Rwork0.2368 10833 -
obs0.2386 11404 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.6 Å2 / Biso mean: 111.131 Å2 / Biso min: 44.06 Å2
Refinement stepCycle: final / Resolution: 3.413→35.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 0 0 5190
Num. residues----672
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.413-3.75610.36711410.3245264097
3.7561-4.29890.27331430.25962713100
4.2989-5.41310.2491430.2131273299
5.4131-35.6030.26211440.2189274899

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