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- PDB-9q9o: TRIM21 PRYSPRY bound to compound 36 -

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Basic information

Entry
Database: PDB / ID: 9q9o
TitleTRIM21 PRYSPRY bound to compound 36
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / E3 ligase / PROTAC / PRYSPRY
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 / protein monoubiquitination / response to type II interferon / positive regulation of protein binding / positive regulation of DNA-binding transcription factor activity / protein K48-linked ubiquitination / proteasomal protein catabolic process / protein autoubiquitination / positive regulation of cell cycle / antiviral innate immune response / positive regulation of autophagy / Regulation of innate immune responses to cytosolic DNA / autophagosome / negative regulation of innate immune response / P-body / protein destabilization / RING-type E3 ubiquitin transferase / protein polyubiquitination / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / 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 / 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: 2.462 Å
AuthorsLuptak, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Development of TRIM21 PROTAC molecules
Authors: Luptak, J. / James, L.C.
History
DepositionFeb 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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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
A: E3 ubiquitin-protein ligase TRIM21
C: E3 ubiquitin-protein ligase TRIM21
D: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1558
Polymers90,0734
Non-polymers2,0834
Water00
1
B: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0392
Polymers22,5181
Non-polymers5211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0392
Polymers22,5181
Non-polymers5211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0392
Polymers22,5181
Non-polymers5211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0392
Polymers22,5181
Non-polymers5211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.685, 74.380, 90.109
Angle α, β, γ (deg.)90.000, 90.103, 90.000
Int Tables number4
Space group name H-MP1211

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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: 22518.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N terminally 6xHis tagged PRYSPRY domain (287-475) of TRIM21
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P19474, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-A1I4Z / 4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]phenyl]methylamino]methyl]-~{N}-methyl-benzamide


Mass: 520.625 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H32N6O2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 5% iso-Propanol, 0.1 M Na Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.46→50.427 Å / Num. obs: 24473 / % possible obs: 83.6 % / Redundancy: 3.1 % / CC1/2: 0.978 / Net I/σ(I): 3
Reflection shellResolution: 2.46→2.56 Å / Num. unique obs: 1326 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.462→50.427 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.842 / SU B: 29.249 / SU ML: 0.561 / Cross valid method: FREE R-VALUE / ESU R Free: 0.5
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.368 1243 5.084 %
Rwork0.3017 23207 -
all0.305 --
obs-24450 83.496 %
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: 34.201 Å2
Baniso -1Baniso -2Baniso -3
1--2.923 Å2-0 Å2-0.364 Å2
2--6.421 Å20 Å2
3----3.496 Å2
Refinement stepCycle: LAST / Resolution: 2.462→50.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 156 0 6064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136292
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155520
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.6438572
X-RAY DIFFRACTIONr_angle_other_deg1.2271.57612724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0525728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00421.882340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.77215916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4731532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2740
X-RAY DIFFRACTIONr_chiral_restr_other0.0140.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021576
X-RAY DIFFRACTIONr_nbd_refined0.2170.21108
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.24876
X-RAY DIFFRACTIONr_nbtor_refined0.180.22791
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.221
X-RAY DIFFRACTIONr_nbd_other0.2560.263
X-RAY DIFFRACTIONr_mcbond_it3.0853.5182924
X-RAY DIFFRACTIONr_mcbond_other3.0843.5172923
X-RAY DIFFRACTIONr_mcangle_it5.0975.2673648
X-RAY DIFFRACTIONr_mcangle_other5.0965.2673649
X-RAY DIFFRACTIONr_scbond_it2.843.7363368
X-RAY DIFFRACTIONr_scbond_other2.843.7363369
X-RAY DIFFRACTIONr_scangle_it4.8465.4784924
X-RAY DIFFRACTIONr_scangle_other4.8465.4784925
X-RAY DIFFRACTIONr_lrange_it10.04965.0824350
X-RAY DIFFRACTIONr_lrange_other10.04965.07924351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.462-2.5260.389470.48787X-RAY DIFFRACTION38.2744
2.526-2.5950.449490.471942X-RAY DIFFRACTION46.8115
2.595-2.670.5430.4441039X-RAY DIFFRACTION53.3531
2.67-2.7520.578630.4311197X-RAY DIFFRACTION63.6364
2.752-2.8420.46750.4391369X-RAY DIFFRACTION76.4831
2.842-2.9420.4571080.4431626X-RAY DIFFRACTION93.7297
2.942-3.0530.4191190.4051665X-RAY DIFFRACTION98.5635
3.053-3.1770.453880.381628X-RAY DIFFRACTION99.019
3.177-3.3180.415800.3541538X-RAY DIFFRACTION98.4185
3.318-3.480.394740.3051495X-RAY DIFFRACTION99.1783
3.48-3.6680.358750.2661431X-RAY DIFFRACTION99.2749
3.668-3.890.304760.2461346X-RAY DIFFRACTION99.2324
3.89-4.1580.353790.2331261X-RAY DIFFRACTION99.1858
4.158-4.490.251530.2091193X-RAY DIFFRACTION99.5208
4.49-4.9180.264490.1981102X-RAY DIFFRACTION99.6537
4.918-5.4960.291590.216997X-RAY DIFFRACTION99.7167
5.496-6.3420.263360.242899X-RAY DIFFRACTION99.7866
6.342-7.7580.294210.217766X-RAY DIFFRACTION99.7465
7.758-10.9310.241350.187584X-RAY DIFFRACTION99.8387

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