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- PDB-7w0t: TRIM7 in complex with C-terminal peptide of 2C -

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Basic information

Entry
Database: PDB / ID: 7w0t
TitleTRIM7 in complex with C-terminal peptide of 2C
Components
  • E3 ubiquitin-protein ligase TRIM7
  • peptide
KeywordsANTIVIRAL PROTEIN
Function / homology
Function and homology information


antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / Golgi apparatus / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger, B-box, chordata / zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. ...Zinc finger, B-box, chordata / zinc finger of C3HC4-type, RING / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM7
Similarity search - Component
Biological speciesHomo sapiens (human)
Coxsackievirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsZhang, H. / Liang, X. / Li, X.Z.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures.
Authors: Liang, X. / Xiao, J. / Li, X. / Liu, Y. / Lu, Y. / Wen, Y. / Li, Z. / Che, X. / Ma, Y. / Zhang, X. / Zhang, Y. / Jian, D. / Wang, P. / Xuan, C. / Yu, G. / Li, L. / Zhang, H.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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
F: E3 ubiquitin-protein ligase TRIM7
C: E3 ubiquitin-protein ligase TRIM7
B: E3 ubiquitin-protein ligase TRIM7
A: peptide
D: peptide
E: peptide


Theoretical massNumber of molelcules
Total (without water)62,3036
Polymers62,3036
Non-polymers00
Water11,259625
1
F: E3 ubiquitin-protein ligase TRIM7
A: peptide


Theoretical massNumber of molelcules
Total (without water)20,7682
Polymers20,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: E3 ubiquitin-protein ligase TRIM7
E: peptide


Theoretical massNumber of molelcules
Total (without water)20,7682
Polymers20,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: E3 ubiquitin-protein ligase TRIM7
D: peptide


Theoretical massNumber of molelcules
Total (without water)20,7682
Polymers20,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.361, 53.758, 81.299
Angle α, β, γ (deg.)90.000, 118.996, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM7 / Glycogenin-interacting protein / RING finger protein 90 / Tripartite motif-containing protein 7


Mass: 19689.295 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7, GNIP, RNF90 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C029, RING-type E3 ubiquitin transferase
#2: Protein/peptide peptide /


Mass: 1078.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Coxsackievirus
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: ammonium acetate, magnesium acetate tetrahydrate, HEPES sodium, polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.569→42.538 Å / Num. obs: 83192 / % possible obs: 99.03 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.96 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.33
Reflection shellResolution: 1.569→1.625 Å / Num. unique obs: 8288 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
PHENIX1.19rc6_4061refinement
PHENIX1.19rc6_4061refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UMA

6uma


Resolution: 1.57→42.45 Å / SU ML: 0.1632 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1864 4264 5.13 %
Rwork0.1683 78918 -
obs0.1693 83182 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.77 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 0 0 625 4819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824305
X-RAY DIFFRACTIONf_angle_d1.00945853
X-RAY DIFFRACTIONf_chiral_restr0.0648632
X-RAY DIFFRACTIONf_plane_restr0.0089763
X-RAY DIFFRACTIONf_dihedral_angle_d6.9561583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.590.24881540.21742542X-RAY DIFFRACTION97.86
1.59-1.610.24351620.20852603X-RAY DIFFRACTION99.6
1.61-1.630.25091060.20172721X-RAY DIFFRACTION99.51
1.63-1.650.26351170.19752586X-RAY DIFFRACTION99.48
1.65-1.670.2494850.19922707X-RAY DIFFRACTION99.18
1.67-1.690.27831110.2322663X-RAY DIFFRACTION99.39
1.69-1.710.23991190.21742654X-RAY DIFFRACTION99.64
1.71-1.740.25821260.20752630X-RAY DIFFRACTION99.46
1.74-1.770.22831520.20292614X-RAY DIFFRACTION99.03
1.77-1.80.23741100.18952630X-RAY DIFFRACTION98.77
1.8-1.830.23121400.17972584X-RAY DIFFRACTION98.8
1.83-1.860.19311900.16912584X-RAY DIFFRACTION98.65
1.86-1.90.18131660.17272559X-RAY DIFFRACTION97.57
1.9-1.930.19291710.19612629X-RAY DIFFRACTION99.72
1.93-1.980.19291430.16872611X-RAY DIFFRACTION99.39
1.98-2.020.20121300.17112615X-RAY DIFFRACTION99.28
2.02-2.070.19841500.16712676X-RAY DIFFRACTION99.68
2.07-2.130.17791520.16932611X-RAY DIFFRACTION99.5
2.13-2.190.20421670.16442607X-RAY DIFFRACTION99.39
2.19-2.260.18671560.18032635X-RAY DIFFRACTION98.62
2.26-2.340.19161480.17052603X-RAY DIFFRACTION98.67
2.34-2.440.19581780.16792560X-RAY DIFFRACTION97.61
2.44-2.550.19151420.16952643X-RAY DIFFRACTION99.43
2.55-2.680.1871970.17632663X-RAY DIFFRACTION99.21
2.68-2.850.19911640.16912641X-RAY DIFFRACTION99.68
2.85-3.070.18671230.17042681X-RAY DIFFRACTION99.68
3.07-3.380.16551380.15222659X-RAY DIFFRACTION97.97
3.38-3.870.15181490.14582620X-RAY DIFFRACTION98.47
3.87-4.870.12941640.13612674X-RAY DIFFRACTION99.58
4.87-42.450.20761540.17092713X-RAY DIFFRACTION98.08
Refinement TLS params.Method: refined / Origin x: -32.9975494094 Å / Origin y: -9.46656087141 Å / Origin z: 20.4040875467 Å
111213212223313233
T0.13106540362 Å20.00681132913878 Å20.000628697048957 Å2-0.108728099041 Å20.000846343689669 Å2--0.11935979721 Å2
L0.286578997653 °20.019477613269 °2-0.018810542929 °2-0.141612231462 °2-0.00703508769302 °2--0.164700622488 °2
S-0.0220820445344 Å °0.023399064002 Å °-0.00882381817769 Å °-0.000777266033709 Å °0.0146787166697 Å °-0.0150873181512 Å °-0.0261963484068 Å °-0.00776347278663 Å °-1.34424395608E-6 Å °
Refinement TLS groupSelection details: all

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