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- PDB-7x70: TRIM7 in complex with C-terminal peptide of NSP8 -

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Basic information

Entry
Database: PDB / ID: 7x70
TitleTRIM7 in complex with C-terminal peptide of NSP8
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)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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
DepositionMar 8, 2022Deposition 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)20,2482
Polymers20,2482
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-3 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.100, 80.100, 53.127
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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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: 558.690 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 49.38 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: Potassium sodium tartrate, Lithium sulfate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→26.22 Å / Num. obs: 46056 / % possible obs: 85.86 % / Redundancy: 2 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.96
Reflection shellResolution: 1.25→1.295 Å / Num. unique obs: 2099 / CC1/2: 0.732

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W0Q

7w0q


Resolution: 1.25→26.22 Å / SU ML: 0.1168 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1703 2205 4.78 %
Rwork0.1419 43889 -
obs0.1433 46051 85.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.76 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 0 242 1633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951446
X-RAY DIFFRACTIONf_angle_d1.121968
X-RAY DIFFRACTIONf_chiral_restr0.0945213
X-RAY DIFFRACTIONf_plane_restr0.0155257
X-RAY DIFFRACTIONf_dihedral_angle_d7.0016199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.2792630.21341149X-RAY DIFFRACTION36.39
1.28-1.310.2502860.18911460X-RAY DIFFRACTION46.32
1.31-1.340.2178880.15951769X-RAY DIFFRACTION55.32
1.34-1.380.18591220.14812226X-RAY DIFFRACTION70.47
1.38-1.420.18621360.14742903X-RAY DIFFRACTION91.12
1.42-1.460.18241270.13443054X-RAY DIFFRACTION95.53
1.46-1.510.17181490.13643078X-RAY DIFFRACTION95.79
1.51-1.570.17831560.13243053X-RAY DIFFRACTION96.11
1.57-1.650.16581250.14043101X-RAY DIFFRACTION96.73
1.65-1.730.17621470.12433121X-RAY DIFFRACTION96.97
1.73-1.840.16541690.13813094X-RAY DIFFRACTION97.26
1.84-1.980.16531580.13293138X-RAY DIFFRACTION97.72
1.98-2.180.15941630.13923146X-RAY DIFFRACTION98.37
2.18-2.50.15631650.14213153X-RAY DIFFRACTION98.57
2.5-3.150.181680.15383187X-RAY DIFFRACTION98.97
3.15-26.220.16561830.14023257X-RAY DIFFRACTION99.71

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