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- PDB-9m3n: Crystal structure of human TRIM21 PRYSPRY in complex with T-02 -

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Basic information

Entry
Database: PDB / ID: 9m3n
TitleCrystal structure of human TRIM21 PRYSPRY in complex with T-02
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / complex / E3 ligase
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 / negative regulation of NF-kappaB transcription factor activity ...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 / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / protein K63-linked ubiquitination / response to type II interferon / protein monoubiquitination / protein K48-linked ubiquitination / proteasomal protein catabolic process / protein autoubiquitination / positive regulation of cell cycle / positive regulation of autophagy / antiviral innate immune response / positive regulation of DNA-binding transcription factor activity / Regulation of innate immune responses to cytosolic DNA / autophagosome / negative regulation of innate immune response / P-body / protein destabilization / RING-type E3 ubiquitin transferase / positive regulation of protein binding / protein polyubiquitination / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / regulation of gene expression / cytoplasmic vesicle / transcription coactivator activity / positive regulation of viral entry into host cell / 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 / Butyrophylin-like, SPRY domain / B-box zinc finger ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / Modified RING finger domain / U-box domain / : / 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
: / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsZhang, L.J. / Zhang, L.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms.
Authors: Zhang, L. / Wang, Q. / Li, X. / Cheng, X. / Cai, L. / Guo, A. / Zhang, L. / Hu, H. / Wu, M. / Li, X. / Li, H. / Meng, X. / Qiu, Y. / Tu, G. / Zhang, L. / Dong, X. / Liang, Y. / Wang, Y. / ...Authors: Zhang, L. / Wang, Q. / Li, X. / Cheng, X. / Cai, L. / Guo, A. / Zhang, L. / Hu, H. / Wu, M. / Li, X. / Li, H. / Meng, X. / Qiu, Y. / Tu, G. / Zhang, L. / Dong, X. / Liang, Y. / Wang, Y. / Li, J. / Dou, D. / Pu, X.
History
DepositionMar 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: 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)20,8212
Polymers20,3941
Non-polymers4271
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.040, 100.040, 50.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 20393.920 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: Homo sapiens (human)
References: UniProt: P19474, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-A1EMT / 1-ethyl-~{N}-methyl-5-phenyl-~{N}-[3-[3-(trifluoromethyl)phenyl]cyclobutyl]pyrazole-4-carboxamide


Mass: 427.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24F3N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.11 Å3/Da / Density % sol: 60.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The solution contained 0.1 M BIS-TRIS propane (pH 7.0) and 1.2 M potassium sodium tartrate tetrahydrate.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.08→35.633 Å / Num. obs: 16022 / % possible obs: 100 % / Redundancy: 1.8 % / CC1/2: 1 / Rmerge(I) obs: 0.017 / Net I/σ(I): 22.3
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.2 / Num. unique obs: 1158 / CC1/2: 0.955 / % possible all: 100

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Processing

Software
NameVersionClassification
xia2data reduction
Aimless0.7.7data scaling
MOLREPphasing
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→35.633 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.08 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2351 826 5.168 %
Rwork0.1912 15156 -
all0.194 --
obs-15982 99.969 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.893 Å2
Baniso -1Baniso -2Baniso -3
1--3.993 Å20 Å20 Å2
2---3.993 Å20 Å2
3---7.986 Å2
Refinement stepCycle: LAST / Resolution: 2.08→35.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 31 45 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131523
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171348
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6452079
X-RAY DIFFRACTIONr_angle_other_deg1.2521.5783111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5325179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61221.97581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28415223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.415158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
X-RAY DIFFRACTIONr_nbd_refined0.1870.2251
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21198
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2701
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.255
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3040.26
X-RAY DIFFRACTIONr_nbd_other0.2640.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.24
X-RAY DIFFRACTIONr_mcbond_it3.8864.797719
X-RAY DIFFRACTIONr_mcbond_other3.8844.795718
X-RAY DIFFRACTIONr_mcangle_it5.3837.187897
X-RAY DIFFRACTIONr_mcangle_other5.3827.189898
X-RAY DIFFRACTIONr_scbond_it4.4615.119804
X-RAY DIFFRACTIONr_scbond_other4.4585.119805
X-RAY DIFFRACTIONr_scangle_it6.7347.5261180
X-RAY DIFFRACTIONr_scangle_other6.7317.5261181
X-RAY DIFFRACTIONr_lrange_it8.88453.7611626
X-RAY DIFFRACTIONr_lrange_other8.88553.6711623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.1340.339590.3361096X-RAY DIFFRACTION100
2.134-2.1930.325500.3161077X-RAY DIFFRACTION100
2.193-2.2560.299550.2781028X-RAY DIFFRACTION100
2.256-2.3260.251530.2321020X-RAY DIFFRACTION100
2.326-2.4020.279470.221990X-RAY DIFFRACTION100
2.402-2.4860.346600.239952X-RAY DIFFRACTION100
2.486-2.580.328550.24909X-RAY DIFFRACTION100
2.58-2.6850.273490.203892X-RAY DIFFRACTION100
2.685-2.8040.237440.217858X-RAY DIFFRACTION100
2.804-2.9410.262430.214824X-RAY DIFFRACTION100
2.941-3.10.267470.207768X-RAY DIFFRACTION100
3.1-3.2880.192390.182743X-RAY DIFFRACTION100
3.288-3.5150.201410.17699X-RAY DIFFRACTION100
3.515-3.7960.239270.166660X-RAY DIFFRACTION100
3.796-4.1580.151320.151625X-RAY DIFFRACTION100
4.158-4.6470.202360.137542X-RAY DIFFRACTION100
4.647-5.3640.231270.148498X-RAY DIFFRACTION100
5.364-6.5650.206300.205423X-RAY DIFFRACTION100
6.565-9.2650.257180.189342X-RAY DIFFRACTION100

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