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- PDB-32qm: Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31) -

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Basic information

Entry
Database: PDB / ID: 32qm
TitleHuman TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / E3-Ligase / PRYSPRY / Inhibitor Complex
Function / homology
Function and homology information


negative regulation of protein deubiquitination / regulation of type I interferon production / suppression of viral release by host / STING mediated induction of host immune responses / negative regulation of viral transcription / cellular response to chemical stress / protein K6-linked ubiquitination / positive regulation of protein binding / protein K27-linked ubiquitination / stress granule disassembly ...negative regulation of protein deubiquitination / regulation of type I interferon production / suppression of viral release by host / STING mediated induction of host immune responses / negative regulation of viral transcription / cellular response to chemical stress / protein K6-linked ubiquitination / positive regulation of protein binding / protein K27-linked ubiquitination / stress granule disassembly / pyroptotic inflammatory response / protein monoubiquitination / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of cell cycle / response to type II interferon / positive regulation of autophagy / negative regulation of innate immune response / autophagosome / Regulation of innate immune responses to cytosolic DNA / antiviral innate immune response / proteasomal protein catabolic process / P-body / protein destabilization / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / Interferon gamma signaling / protein polyubiquitination / 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 / nucleoplasm / zinc ion binding / 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: 1.5 Å
AuthorsKim, Y. / Schallmayer, L. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
Authors: Kim, Y. / Schallmayer, L. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionJul 21, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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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)21,0773
Polymers20,5511
Non-polymers5262
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.593, 64.593, 73.527
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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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: 20551.131 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A1KEE / ~{N}-[(1~{R})-1-cyclohexylethyl]-4-(4-fluoranyl-2-methylsulfanyl-phenyl)-~{N}-methyl-2-methylsulfonyl-benzamide


Mass: 463.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30FNO3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 293 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 XE 16M / Detector: PIXEL / Date: Aug 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→55.94 Å / Num. obs: 27917 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.011 / Rrim(I) all: 0.052 / Χ2: 0.91 / Net I/σ(I): 29.5 / Num. measured all: 580208
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 99.7 % / Redundancy: 20.9 % / Rmerge(I) obs: 1.079 / Num. measured all: 28264 / Num. unique obs: 1351 / CC1/2: 0.865 / Rpim(I) all: 0.239 / Rrim(I) all: 1.106 / Χ2: 0.77 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→55.94 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.649 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19636 1353 4.9 %RANDOM
Rwork0.16352 ---
obs0.16511 26530 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.531 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 1.5→55.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 35 81 1539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121537
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161346
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.7872104
X-RAY DIFFRACTIONr_angle_other_deg0.5241.7653103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.56858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24610214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
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_it6.522.678734
X-RAY DIFFRACTIONr_mcbond_other6.4952.677734
X-RAY DIFFRACTIONr_mcangle_it9.5444.819921
X-RAY DIFFRACTIONr_mcangle_other9.5444.82922
X-RAY DIFFRACTIONr_scbond_it6.2732.815803
X-RAY DIFFRACTIONr_scbond_other6.2692.815804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1835.0731184
X-RAY DIFFRACTIONr_long_range_B_refined13.64728.361636
X-RAY DIFFRACTIONr_long_range_B_other13.64528.351637
X-RAY DIFFRACTIONr_rigid_bond_restr2.97832883
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 102 -
Rwork0.19 1948 -
obs--99.95 %

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