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- PDB-32qp: Human TRIM21 PRYSPRY domain in complex with PRLX-93936 -

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Basic information

Entry
Database: PDB / ID: 32qp
TitleHuman TRIM21 PRYSPRY domain in complex with PRLX-93936
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: 2.1 Å
AuthorsKim, Y. / 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 PRLX-93936
Authors: Kim, Y. / 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)23,3872
Polymers23,0231
Non-polymers3641
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.613, 59.613, 169.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 23022.811 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-A1KEH / 3-(2-ethoxyphenyl)-2-(piperazin-1-ylmethyl)quinazolin-4-one


Mass: 364.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4.3 M Sodium Chloride 0.1 M Hepes pH8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→56.24 Å / Num. obs: 18781 / % possible obs: 100 % / Redundancy: 25.9 % / CC1/2: 1 / Net I/σ(I): 17.7
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 1508 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.844 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 935 5 %RANDOM
Rwork0.20575 ---
obs0.20734 17765 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0 Å20 Å2
2--0.67 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 27 44 1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121522
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161336
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.7832077
X-RAY DIFFRACTIONr_angle_other_deg0.5061.7583076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6825179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.18957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80510212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
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_it3.364.723722
X-RAY DIFFRACTIONr_mcbond_other3.364.723722
X-RAY DIFFRACTIONr_mcangle_it4.968.456899
X-RAY DIFFRACTIONr_mcangle_other4.9628.459900
X-RAY DIFFRACTIONr_scbond_it3.9895.021800
X-RAY DIFFRACTIONr_scbond_other3.9875.02801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1099.0471179
X-RAY DIFFRACTIONr_long_range_B_refined8.13345.891608
X-RAY DIFFRACTIONr_long_range_B_other8.12945.891608
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 62 -
Rwork0.312 1297 -
obs--99.93 %

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