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- PDB-7qs2: Crystal structure of B30.2 PRYSPRY domain of TRIM15 -

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Basic information

Entry
Database: PDB / ID: 7qs2
TitleCrystal structure of B30.2 PRYSPRY domain of TRIM15
ComponentsTRIM15
KeywordsLIGASE / E3 / TRIM / TRIM15 / B30.2 domain / SPRY domain / PRYSPRY domain
Function / homology
Function and homology information


zinc ion binding / nucleus / cytoplasm
Similarity search - Function
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 / : / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: TRIM15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,67518
Polymers19,3611
Non-polymers1,31517
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.764, 54.764, 125.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TRIM15 / Tripartite motif-containing protein 15


Mass: 19360.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM15 / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: A0A0G2JJP1
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
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 iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.7→41.23 Å / Num. obs: 21814 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.035 / Rrim(I) all: 0.123 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7412.51.2212.212670.7670.3521.174100
8.5-41.239.50.0452280.9980.0150.04899.4

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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: 6umb

6umb


Resolution: 1.7→41.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.971 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1043 4.8 %RANDOM
Rwork0.1688 ---
obs0.1703 20730 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.76 Å2 / Biso mean: 22.272 Å2 / Biso min: 11.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.7→41.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 56 102 1468
Biso mean--37.78 33.19 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171376
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6581918
X-RAY DIFFRACTIONr_angle_other_deg1.3481.5783175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5145189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.77320.88268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3971511
X-RAY DIFFRACTIONr_chiral_restr0.0960.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021604
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02330
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 83 -
Rwork0.225 1476 -
all-1559 -
obs--100 %
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)
10.83840.0136-0.19120.95390.20280.94480.00590.1158-0.0672-0.0581-0.01050.00460.0020.05690.00460.01370.00820.00050.0274-0.00980.00588.718830.93845.7003
21.0990.194-0.69140.40630.06971.5297-0.0151-0.1006-0.05260.0446-0.0106-0.03550.06290.12370.02570.0186-0.00360.00540.0175-0.00050.009811.440831.889358.7497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A292 - 380
2X-RAY DIFFRACTION2A381 - 465

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