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- PDB-7w0q: TRIM7 in complex with C-terminal peptide of 2C -

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Basic information

Entry
Database: PDB / ID: 7w0q
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: 1.1 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM7
B: peptide


Theoretical massNumber of molelcules
Total (without water)20,7682
Polymers20,7682
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-1 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.486, 53.178, 46.744
Angle α, β, γ (deg.)90.000, 91.437, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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.: 1
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.: 1 / Source method: obtained synthetically / Source: (synth.) Coxsackievirus
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion / Details: PEG 3350, potassium nitrate

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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: 1.1→46.73 Å / Num. obs: 60806 / % possible obs: 86.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.69
Reflection shellResolution: 1.1→1.139 Å / Num. unique obs: 3023 / CC1/2: 0.974

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Processing

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

6uma


Resolution: 1.1→46.73 Å / SU ML: 0.0927 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 20.6866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 3071 5.05 %
Rwork0.1857 57733 -
obs0.187 60804 86.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.02 Å2
Refinement stepCycle: LAST / Resolution: 1.1→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 0 226 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791504
X-RAY DIFFRACTIONf_angle_d1.18472045
X-RAY DIFFRACTIONf_chiral_restr0.0956222
X-RAY DIFFRACTIONf_plane_restr0.0115267
X-RAY DIFFRACTIONf_dihedral_angle_d7.1376205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.2753690.26481018X-RAY DIFFRACTION34.5
1.11-1.130.2488810.21541445X-RAY DIFFRACTION47.14
1.13-1.150.27181000.20851685X-RAY DIFFRACTION57.05
1.15-1.170.18181110.20832155X-RAY DIFFRACTION70.81
1.17-1.20.20381300.19072575X-RAY DIFFRACTION84.11
1.2-1.220.24811310.19612841X-RAY DIFFRACTION93.75
1.22-1.250.2131490.19252971X-RAY DIFFRACTION97.68
1.25-1.280.23231320.18982980X-RAY DIFFRACTION97.74
1.28-1.310.21531540.18962960X-RAY DIFFRACTION97.86
1.31-1.340.16981660.18222968X-RAY DIFFRACTION97.72
1.34-1.380.20211660.18952996X-RAY DIFFRACTION97.96
1.38-1.430.19521660.18562959X-RAY DIFFRACTION98.46
1.43-1.480.20661560.18493018X-RAY DIFFRACTION98.69
1.48-1.540.2271550.1762953X-RAY DIFFRACTION98.54
1.54-1.610.18241550.17793003X-RAY DIFFRACTION98.11
1.61-1.690.20511760.17722986X-RAY DIFFRACTION99.25
1.69-1.80.18941710.18333018X-RAY DIFFRACTION99.16
1.8-1.940.21171060.18082324X-RAY DIFFRACTION75.49
1.94-2.130.22321180.17582499X-RAY DIFFRACTION81.81
2.13-2.440.22431500.18842692X-RAY DIFFRACTION87.74
2.44-3.070.26211520.20222813X-RAY DIFFRACTION91.94
3.08-46.730.18911770.17642874X-RAY DIFFRACTION92.65
Refinement TLS params.Method: refined / Origin x: 13.7605995261 Å / Origin y: 13.7370427712 Å / Origin z: 12.9602185845 Å
111213212223313233
T0.0612206743401 Å20.00933636259431 Å20.00773301657356 Å2-0.0671812210932 Å2-0.0098897182442 Å2--0.0616651974065 Å2
L0.88899140653 °20.528361840559 °20.327671012782 °2-1.13345880215 °2-0.0920123393695 °2--0.701212707968 °2
S-0.0105191049795 Å °0.0868596680506 Å °-0.0340232743791 Å °0.0244740120024 Å °0.0321300534845 Å °-0.0904742918626 Å °0.0161919432903 Å °-0.000371822749312 Å °0.229053340117 Å °
Refinement TLS groupSelection details: all

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