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- PDB-9ii5: Crystal structure of human TRIM21 PRYSPRY in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 9ii5
TitleCrystal structure of human TRIM21 PRYSPRY in complex with compound 1
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / complex / E3 ligase
Function / homology
Function and homology information


negative regulation of protein deubiquitination / regulation of type I interferon production / suppression of viral release by host / STING mediated induction of host immune responses / negative regulation of viral transcription / cellular response to chemical stress / protein K6-linked ubiquitination / positive regulation of protein binding / protein K27-linked ubiquitination / stress granule disassembly ...negative regulation of protein deubiquitination / regulation of type I interferon production / suppression of viral release by host / STING mediated induction of host immune responses / negative regulation of viral transcription / cellular response to chemical stress / protein K6-linked ubiquitination / positive regulation of protein binding / protein K27-linked ubiquitination / stress granule disassembly / pyroptotic inflammatory response / protein monoubiquitination / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of cell cycle / response to type II interferon / negative regulation of innate immune response / positive regulation of autophagy / autophagosome / Regulation of innate immune responses to cytosolic DNA / antiviral innate immune response / proteasomal protein catabolic process / P-body / protein destabilization / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / Interferon gamma signaling / protein polyubiquitination / cytoplasmic stress granule / ubiquitin-protein transferase activity / regulation of gene expression / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / cytoplasmic vesicle / positive regulation of viral entry into host cell / transcription coactivator activity / protein ubiquitination / ribonucleoprotein complex / innate immune response / DNA binding / RNA binding / nucleoplasm / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / Modified RING finger domain / U-box domain / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / Modified RING finger domain / U-box domain / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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 TRIM21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsZhang, L.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Chemically Induced Nuclear Pore Complex Protein Degradation via TRIM21.
Authors: Li, X. / Wang, Q. / Guo, A. / Qiu, Y. / Chen, Q. / Li, Y. / Zhang, L. / Guo, Y. / Meng, X. / Li, S. / Liu, G. / Zhang, L. / Liu, J. / Li, X. / Cai, L. / Cheng, X. / Liu, C. / Wang, X. / ...Authors: Li, X. / Wang, Q. / Guo, A. / Qiu, Y. / Chen, Q. / Li, Y. / Zhang, L. / Guo, Y. / Meng, X. / Li, S. / Liu, G. / Zhang, L. / Liu, J. / Li, X. / Cai, L. / Cheng, X. / Liu, C. / Wang, X. / Wood, A. / Murray, J. / Liu, G. / Li, J. / Huang, X. / Dou, D.
History
DepositionJun 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6432
Polymers20,1941
Non-polymers4501
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.340, 65.340, 71.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-662-

HOH

21A-692-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM21 / 52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / Ro(SS-A) ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 20193.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Production host: Homo sapiens (human)
References: UniProt: P19474, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-A1D9F / ~{N}-[(1-fluoranylcyclohexyl)methyl]-~{N}-methyl-4-(2-methylsulfanylphenyl)-2-methylsulfonyl-benzamide


Mass: 449.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28FNO3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 1. Cryo buffer: 80 uL TRIM21 (Reservoir Solution: 0.1 M Cirtic, pH 3.5, 3 M NaCl) + 20 uL glycerol 2. Soaked crystals in cryo buffer for 10s

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.49→26.31 Å / Num. obs: 28307 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 22.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.3
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.277 / Num. unique obs: 2052 / CC1/2: 0.55 / % possible all: 99.6

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→24.12 Å / SU ML: 0.1816 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 27.772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 1388 4.91 %
Rwork0.2123 26894 -
obs0.2136 28282 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.24 Å2
Refinement stepCycle: LAST / Resolution: 1.49→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 30 92 1549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671507
X-RAY DIFFRACTIONf_angle_d0.98042056
X-RAY DIFFRACTIONf_chiral_restr0.0932207
X-RAY DIFFRACTIONf_plane_restr0.008264
X-RAY DIFFRACTIONf_dihedral_angle_d6.7145201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.540.30581390.27682627X-RAY DIFFRACTION99.71
1.54-1.610.26031700.24392654X-RAY DIFFRACTION99.72
1.61-1.680.27191280.24092700X-RAY DIFFRACTION99.89
1.68-1.770.24561280.2342716X-RAY DIFFRACTION99.89
1.77-1.880.26211190.23692676X-RAY DIFFRACTION99.93
1.88-2.020.22371490.21472687X-RAY DIFFRACTION100
2.02-2.230.31831310.22662707X-RAY DIFFRACTION100
2.23-2.550.28811420.22482683X-RAY DIFFRACTION100
2.55-3.210.23481440.22892698X-RAY DIFFRACTION100
3.21-24.120.20281380.1832746X-RAY DIFFRACTION99.86

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