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- PDB-7b2s: Crystal structure of SPRY domain of TRIM9 -

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Basic information

Entry
Database: PDB / ID: 7b2s
TitleCrystal structure of SPRY domain of TRIM9
ComponentsE3 ubiquitin-protein ligase TRIM9
KeywordsLIGASE / E3 ligase / SPRY domain / TRIM / protein-protein interaction / B30.2/SPRY / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RING-type E3 ubiquitin transferase / synaptic vesicle / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / protein domain specific binding / dendrite / protein homodimerization activity ...RING-type E3 ubiquitin transferase / synaptic vesicle / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / protein domain specific binding / dendrite / protein homodimerization activity / zinc ion binding / cytoplasm
Similarity search - Function
: / COS domain / COS domain profile. / : / ANCHR-like B-box zinc-binding domain / B-box, C-terminal / B-Box C-terminal domain / SPRY domain / B-box zinc finger / B-Box-type zinc finger ...: / COS domain / COS domain profile. / : / ANCHR-like B-box zinc-binding domain / B-box, C-terminal / B-Box C-terminal domain / 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. / Fibronectin type III domain / Ring finger / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
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
DepositionNov 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: E3 ubiquitin-protein ligase TRIM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0452
Polymers19,9491
Non-polymers961
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-6 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.620, 45.280, 57.657
Angle α, β, γ (deg.)90.000, 106.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-801-

SO4

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM9 / RING finger protein 91 / RING-type E3 ubiquitin transferase TRIM9 / Tripartite motif-containing protein 9


Mass: 19949.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM9, KIAA0282, RNF91 / Plasmid: pGTVL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q9C026, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.93 Å3/Da / Density % sol: 36.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 8000, 0.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.5→35.91 Å / Num. obs: 24080 / % possible obs: 98.6 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.015 / Rrim(I) all: 0.036 / Net I/σ(I): 33.9
Reflection shell

CC1/2: 0.995 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.5-1.545.40.05619.517600.0290.06997.6
6.71-35.914.70.0412820.0210.04694.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x8n

4x8n


Resolution: 1.5→35.91 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.037 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0692 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1738 1201 5 %RANDOM
Rwork0.1416 ---
obs0.1432 22878 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.47 Å2 / Biso mean: 14.448 Å2 / Biso min: 5.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0.28 Å2
2--0.2 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.5→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 5 239 1607
Biso mean--35.44 27.01 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171318
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6351993
X-RAY DIFFRACTIONr_angle_other_deg1.4271.5843032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6095187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.70322.68382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63515229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.337158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 84 -
Rwork0.151 1674 -
all-1758 -
obs--97.34 %
Refinement TLS params.Method: refined / Origin x: 3.6472 Å / Origin y: 17.8448 Å / Origin z: 40.418 Å
111213212223313233
T0.0094 Å20.0018 Å2-0.0036 Å2-0.0084 Å2-0.0025 Å2--0.0024 Å2
L0.6082 °2-0.252 °20.0016 °2-0.43 °2-0.0793 °2--0.8074 °2
S0.0018 Å °-0.0184 Å °-0.0035 Å °0.0416 Å °-0.0041 Å °-0.0033 Å °-0.0146 Å °0.0575 Å °0.0023 Å °

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