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- PDB-9qba: Human TRIM21 PRYSPRY domain in complex with AL236 -

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Basic information

Entry
Database: PDB / ID: 9qba
TitleHuman TRIM21 PRYSPRY domain in complex with AL236
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / PRYSPRY Domain / E3 ligase / Inhibitor
Function / homology
Function and homology information


suppression of viral release by host / protein K27-linked ubiquitination / negative regulation of protein deubiquitination / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / cellular response to chemical stress / stress granule disassembly / : ...suppression of viral release by host / protein K27-linked ubiquitination / negative regulation of protein deubiquitination / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / cellular response to chemical stress / stress granule disassembly / : / pyroptotic inflammatory response / protein K63-linked ubiquitination / protein monoubiquitination / positive regulation of protein binding / response to type II interferon / : / protein K48-linked ubiquitination / protein autoubiquitination / proteasomal protein catabolic process / positive regulation of cell cycle / antiviral innate immune response / positive regulation of autophagy / autophagosome / Regulation of innate immune responses to cytosolic DNA / negative regulation of innate immune response / P-body / RING-type E3 ubiquitin transferase / protein destabilization / protein polyubiquitination / Interferon gamma signaling / cytoplasmic stress granule / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / regulation of gene expression / cytoplasmic vesicle / positive regulation of viral entry into host cell / transcription coactivator activity / protein ubiquitination / ribonucleoprotein complex / innate immune response / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / Modified RING finger domain / U-box domain / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / Modified RING finger domain / U-box domain / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain / 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
: / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKim, Y. / Lucic, A. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: Commun Chem / Year: 2025
Title: Crystallographic fragment screening reveals ligand hotspots in TRIM21 PRY-SPRY domain.
Authors: Kim, Y. / Lucic, A. / Lenz, C. / Farges, F. / Schwalm, M.P. / Saxena, K. / Hanke, T. / Marples, P.G. / Aschenbrenner, J.C. / Fearon, D. / von Delft, F. / Kramer, A. / Knapp, S.
History
DepositionMar 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Sep 24, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,8934
Polymers20,3331
Non-polymers5603
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint6 kcal/mol
Surface area8530 Å2
Unit cell
Length a, b, c (Å)67.750, 67.750, 71.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM21 / 52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / Ro(SS-A) ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 20332.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Production host: Escherichia coli (E. coli)
References: UniProt: P19474, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-A1I41 / ~{N}-(cyclohexylmethyl)-4-(4-fluoranyl-2-methylsulfanyl-phenyl)-2-methylsulfonyl-benzamide


Mass: 435.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26FNO3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 2.3 M Sodium Chloride 0.1 M Sodium Citrate

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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 X 16M / Detector: PIXEL / Date: Feb 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.45→58.67 Å / Num. obs: 32898 / % possible obs: 100 % / Redundancy: 20.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Χ2: 0.92 / Net I/σ(I): 19.5 / Num. measured all: 681895
Reflection shellResolution: 1.45→1.47 Å / % possible obs: 100 % / Redundancy: 19.4 % / Rmerge(I) obs: 1.516 / Num. measured all: 31898 / Num. unique obs: 1643 / CC1/2: 0.819 / Rpim(I) all: 0.349 / Rrim(I) all: 1.557 / Χ2: 0.84 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→58.67 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.506 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.162 1571 4.8 %RANDOM
Rwork0.15044 ---
obs0.15102 31293 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.862 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.2 Å2-0 Å2
2---0.39 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.45→58.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 37 123 1578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121511
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161331
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.7882061
X-RAY DIFFRACTIONr_angle_other_deg0.4911.7653070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.395179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.23758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21710213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
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_it4.0162.173716
X-RAY DIFFRACTIONr_mcbond_other3.9742.172716
X-RAY DIFFRACTIONr_mcangle_it6.2073.916895
X-RAY DIFFRACTIONr_mcangle_other6.213.916896
X-RAY DIFFRACTIONr_scbond_it4.1732.338795
X-RAY DIFFRACTIONr_scbond_other4.172.34796
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3364.1961167
X-RAY DIFFRACTIONr_long_range_B_refined10.80924.041669
X-RAY DIFFRACTIONr_long_range_B_other10.61123.671652
X-RAY DIFFRACTIONr_rigid_bond_restr1.92432842
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 91 -
Rwork0.214 2345 -
obs--100 %

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