[English] 日本語
Yorodumi
- PDB-7qs1: Crystal structure of B30.2 PRYSPRY domain of TRIM11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qs1
TitleCrystal structure of B30.2 PRYSPRY domain of TRIM11
ComponentsE3 ubiquitin-protein ligase TRIM11
KeywordsLIGASE / E3 / TRIM / TRIM11 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / suppression of viral release by host / host-mediated suppression of symbiont invasion / negative regulation of viral transcription / protein autoubiquitination / RING-type E3 ubiquitin transferase / negative regulation of neurogenesis / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...negative regulation of AIM2 inflammasome complex assembly / suppression of viral release by host / host-mediated suppression of symbiont invasion / negative regulation of viral transcription / protein autoubiquitination / RING-type E3 ubiquitin transferase / negative regulation of neurogenesis / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of gene expression / protein-macromolecule adaptor activity / positive regulation of viral entry into host cell / protein ubiquitination / protein domain specific binding / innate immune response / negative regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
zinc finger of C3HC4-type, RING / SPRY 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 of C3HC4-type, RING / SPRY 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. / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsChaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Struct Biol X / Year: 2025
Title: Structural analysis of TRIM family PRYSPRY domains and its implications for E3-ligand design.
Authors: Zhubi, R. / Chaikuad, A. / Munoz Sosa, C.J. / Joerger, A.C. / Knapp, S.
History
DepositionJan 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Sep 10, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM11
B: E3 ubiquitin-protein ligase TRIM11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,75816
Polymers41,7872
Non-polymers97114
Water2,360131
1
A: E3 ubiquitin-protein ligase TRIM11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2726
Polymers20,8941
Non-polymers3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase TRIM11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,48610
Polymers20,8941
Non-polymers5939
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.636, 42.018, 68.584
Angle α, β, γ (deg.)90.000, 99.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 276 - 459 / Label seq-ID: 2 - 185

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein E3 ubiquitin-protein ligase TRIM11 / Protein BIA1 / RING finger protein 92 / RING-type E3 ubiquitin transferase TRIM11 / Tripartite ...Protein BIA1 / RING finger protein 92 / RING-type E3 ubiquitin transferase TRIM11 / Tripartite motif-containing protein 11


Mass: 20893.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM11, RNF92 / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q96F44, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 10% ethylene glycol, 0.2M sodium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→43.36 Å / Num. obs: 27861 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.032 / Rrim(I) all: 0.078 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1 / % possible all: 99.4

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.93-26.10.764227300.7940.3690.921
7.47-43.365.60.0385330.9980.0170.042

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2iwg

2iwg


Resolution: 1.93→43.36 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.779 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1523 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1407 5.1 %RANDOM
Rwork0.1683 ---
obs0.1702 26443 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.75 Å2 / Biso mean: 44.167 Å2 / Biso min: 25.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.56 Å2
2--1.33 Å20 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 1.93→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 59 131 3019
Biso mean--61.19 48.73 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172759
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6643997
X-RAY DIFFRACTIONr_angle_other_deg1.2511.5766352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2475360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.17219.318176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7315458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6761537
X-RAY DIFFRACTIONr_chiral_restr0.0710.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023302
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02728
Refine LS restraints NCS

Ens-ID: 1 / Number: 5076 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 114 -
Rwork0.236 1932 -
all-2046 -
obs--99.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3744-0.0685-0.90320.84971.19053.5277-0.03390.0458-0.0346-0.0731-0.09080.063-0.0885-0.25210.12470.096-0.0162-0.00990.16610.00980.057673.55792.828951.6436
24.7378-1.47672.97152.01431.07585.5174-0.1516-0.26420.40440.06430.12560.0192-0.24540.16960.0260.0987-0.06730.01870.1332-0.08380.238446.955810.588748.287
32.0922-0.5806-1.0141.16360.55953.0133-0.01480.1046-0.04290.1089-0.19960.0930.0303-0.43650.21440.0533-0.0437-0.00350.2499-0.01690.024267.5324.613758.1332
40.7012-0.1074-0.37570.5912-0.19981.48670.0488-0.02170.0673-0.0056-0.03570.03470.04970.0255-0.01310.0621-0.01050.01160.11750.0090.035636.8741-4.976144.1073
57.997-2.9991-3.9061.61812.53614.5097-0.29610.6179-0.17150.14580.02170.22760.20950.38720.27440.1117-0.02240.01330.30580.01450.161754.4738-1.440940.2194
61.3356-0.1003-0.31541.18970.10611.6999-0.0114-0.10450.0270.1381-0.02790.01980.03490.1080.03930.0679-0.03530.00690.1444-0.00420.012540.8914-3.190551.9966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A276 - 381
2X-RAY DIFFRACTION2A382 - 400
3X-RAY DIFFRACTION3A401 - 459
4X-RAY DIFFRACTION4B276 - 380
5X-RAY DIFFRACTION5B381 - 398
6X-RAY DIFFRACTION6B399 - 459

+
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