[English] 日本語
Yorodumi
- PDB-9ii5: Crystal structure of human TRIM21 PRYSPRY in complex with compound 1 -

+
Open data


ID or keywords:

Loading...

-
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


suppression of viral release by host / protein K27-linked ubiquitination / negative regulation of protein deubiquitination / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / cellular response to chemical stress / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity ...suppression of viral release by host / protein K27-linked ubiquitination / negative regulation of protein deubiquitination / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / cellular response to chemical stress / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / protein K63-linked ubiquitination / protein monoubiquitination / response to type II interferon / positive regulation of protein binding / positive regulation of DNA-binding transcription factor activity / protein K48-linked ubiquitination / Regulation of innate immune responses to cytosolic DNA / proteasomal protein catabolic process / protein autoubiquitination / positive regulation of cell cycle / antiviral innate immune response / positive regulation of autophagy / autophagosome / negative regulation of innate immune response / P-body / protein destabilization / RING-type E3 ubiquitin transferase / KEAP1-NFE2L2 pathway / protein polyubiquitination / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / regulation of gene expression / cytoplasmic vesicle / positive regulation of viral entry into host cell / transcription coactivator activity / protein ubiquitination / ribonucleoprotein complex / innate immune response / DNA binding / RNA binding / zinc ion binding / nucleoplasm / 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 / Butyrophylin-like, SPRY domain / B-box zinc finger ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / Modified RING finger domain / U-box domain / 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, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more