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- PDB-7qs3: Crystal structure of B30.2 PRYSPRY domain of TRIM16 -

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Basic information

Entry
Database: PDB / ID: 7qs3
TitleCrystal structure of B30.2 PRYSPRY domain of TRIM16
ComponentsTripartite motif-containing protein 16
KeywordsLIGASE / E3 / TRIM / TRIM16 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


response to organophosphorus / positive regulation of retinoic acid receptor signaling pathway / NACHT domain binding / interleukin-1 binding / positive regulation of keratinocyte differentiation / response to growth hormone / response to retinoic acid / positive regulation of interleukin-1 beta production / PML body / RING-type E3 ubiquitin transferase ...response to organophosphorus / positive regulation of retinoic acid receptor signaling pathway / NACHT domain binding / interleukin-1 binding / positive regulation of keratinocyte differentiation / response to growth hormone / response to retinoic acid / positive regulation of interleukin-1 beta production / PML body / RING-type E3 ubiquitin transferase / transferase activity / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 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 ...: / 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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Tripartite motif-containing protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChaikuad, A. / Zhubi, R. / 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 / pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,54017
Polymers24,5741
Non-polymers96616
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.730, 55.730, 159.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tripartite motif-containing protein 16 / E3 ubiquitin-protein ligase TRIM16 / Estrogen-responsive B box protein


Mass: 24573.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM16, EBBP / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O95361, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.2M sodium bromide

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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: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→45.69 Å / Num. obs: 26339 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.021 / Rrim(I) all: 0.065 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.819.10.9922.325090.9150.3661.12399.9
6.78-45.697.70.0425650.9990.0160.04599.8

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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: 6flm

6flm


Resolution: 1.75→45.69 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.612 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 1246 4.7 %RANDOM
Rwork0.163 ---
obs0.1647 25014 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.71 Å2 / Biso mean: 38.628 Å2 / Biso min: 23.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å2-0 Å2-0 Å2
2--1.4 Å2-0 Å2
3----2.81 Å2
Refinement stepCycle: final / Resolution: 1.75→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 61 149 1814
Biso mean--53.08 46.53 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131727
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171583
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6712320
X-RAY DIFFRACTIONr_angle_other_deg1.3311.5743649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9315200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.41421.81899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63315272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1961511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021911
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02431
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 83 -
Rwork0.261 1829 -
all-1912 -
obs--99.9 %
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)
14.47680.7490.45955.984-2.87999.9859-0.17520.4030.6331-0.61310.14530.3943-0.2892-0.43750.02990.16170.0886-0.02360.20560.05520.2235-5.533743.798748.6196
21.1216-0.07060.17732.0629-0.77272.4220.02920.06490.0216-0.08160.05220.0880.0094-0.2562-0.08140.00430.0048-0.00270.06870.00350.00673.924928.037355.3764
35.9706-3.7951.05494.2805-0.7431.043-0.0288-0.00650.28590.1218-0.0235-0.0986-0.1309-0.07930.05230.1274-0.01360.0070.15270.00840.11575.348834.986664.1038
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A358 - 375
2X-RAY DIFFRACTION2A376 - 537
3X-RAY DIFFRACTION3A538 - 550

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