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- PDB-9gte: Crystal structure of TRIM21 PRY-SPRY domain bound to Suramin -

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Basic information

Entry
Database: PDB / ID: 9gte
TitleCrystal structure of TRIM21 PRY-SPRY domain bound to Suramin
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / PRY-SPRY domain / Suramin / E3 Ligase
Function / homology
Function and homology information


negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity / response to type II interferon / protein K63-linked ubiquitination / protein monoubiquitination / protein autoubiquitination ...negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity / response to type II interferon / protein K63-linked ubiquitination / protein monoubiquitination / protein autoubiquitination / positive regulation of cell cycle / positive regulation of autophagy / autophagosome / negative regulation of innate immune response / P-body / protein destabilization / RING-type E3 ubiquitin transferase / protein polyubiquitination / cytoplasmic stress granule / ubiquitin-protein transferase activity / positive regulation of protein binding / ubiquitin protein ligase activity / cytoplasmic vesicle / protein ubiquitination / ribonucleoprotein complex / DNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / 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
Chem-SVR / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKim, Y. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: LOPAC library screening identifies suramin as a TRIM21 binder with a unique binding mode revealed by crystal structure.
Authors: Kim, Y. / Knapp, S. / Kramer, A.
History
DepositionSep 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2668
Polymers21,5961
Non-polymers1,6707
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-7 kcal/mol
Surface area9790 Å2
Unit cell
Length a, b, c (Å)42.591, 56.014, 69.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM21 / 52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / Ro(SS-A) / Sjoegren syndrome ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 21596.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim21, Ro52, Ssa1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q62191, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN


Mass: 1297.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.91 Å3/Da / Density % sol: 35.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% PEG 6.000 10% ethylene glycol 0.2 ammonium Chlorid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→69.01 Å / Num. obs: 41260 / % possible obs: 99.7 % / Redundancy: 22.8 % / CC1/2: 0.999 / Net I/σ(I): 22.1
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1896 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→43.49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.765 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17898 2020 4.9 %RANDOM
Rwork0.15914 ---
obs0.16012 39175 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.374 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å2-0 Å2
2---0.64 Å20 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 1.3→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 110 151 1744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121701
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161440
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.7462335
X-RAY DIFFRACTIONr_angle_other_deg0.4571.6133300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.36859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.110234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022063
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02433
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0371.138774
X-RAY DIFFRACTIONr_mcbond_other2.0241.138774
X-RAY DIFFRACTIONr_mcangle_it3.2862.045978
X-RAY DIFFRACTIONr_mcangle_other3.2862.047979
X-RAY DIFFRACTIONr_scbond_it2.5141.297927
X-RAY DIFFRACTIONr_scbond_other2.4971.296923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8232.3091352
X-RAY DIFFRACTIONr_long_range_B_refined10.08715.492005
X-RAY DIFFRACTIONr_long_range_B_other10.08615.492006
X-RAY DIFFRACTIONr_rigid_bond_restr2.39833141
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 132 -
Rwork0.214 2766 -
obs--95.52 %

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