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- PDB-9q9p: TRIM21 PRYSPRY bound to compound 37 -

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Basic information

Entry
Database: PDB / ID: 9q9p
TitleTRIM21 PRYSPRY bound to compound 37
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: 2.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0542
Polymers22,5181
Non-polymers5361
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, technically fluorescent polarisation experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9020 Å2
Unit cell
Length a, b, c (Å)37.104, 60.620, 41.931
Angle α, β, γ (deg.)90.000, 113.010, 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.: 1
Source method: isolated from a genetically manipulated source
Details: 6xHis tagged PRYSPRY domain (287-475) of human 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-A1I4X / (2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(2-methoxyphenyl)propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide


Mass: 535.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H41N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG 10000, 0.1 M TRIS HCl pH 8.5

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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 PILATUS3 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: 2.1→38.624 Å / Num. obs: 10082 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.959 / Net I/σ(I): 4.8
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 809 / CC1/2: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2.multiplexdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.624 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.946 / SU ML: 0.311 / Cross valid method: FREE R-VALUE / ESU R: 0.334 / ESU R Free: 0.254
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2965 447 4.441 %
Rwork0.2315 9619 -
all0.235 --
obs-10066 99.98 %
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: 32.481 Å2
Baniso -1Baniso -2Baniso -3
1--1.668 Å20 Å21.299 Å2
2---1.293 Å2-0 Å2
3---1.365 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 39 31 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131580
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151400
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6422152
X-RAY DIFFRACTIONr_angle_other_deg1.1561.5773234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4995183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79721.60987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54615231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.848158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_nbd_refined0.2050.2320
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21326
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2725
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2704
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0950.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.214
X-RAY DIFFRACTIONr_nbd_other0.2350.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3840.22
X-RAY DIFFRACTIONr_mcbond_it2.0593.379735
X-RAY DIFFRACTIONr_mcbond_other2.0543.378734
X-RAY DIFFRACTIONr_mcangle_it3.3295.065917
X-RAY DIFFRACTIONr_mcangle_other3.3295.066918
X-RAY DIFFRACTIONr_scbond_it1.9713.552845
X-RAY DIFFRACTIONr_scbond_other1.973.551846
X-RAY DIFFRACTIONr_scangle_it3.2045.2491235
X-RAY DIFFRACTIONr_scangle_other3.2035.2491236
X-RAY DIFFRACTIONr_lrange_it5.16438.811731
X-RAY DIFFRACTIONr_lrange_other5.14838.8071731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.384370.344698X-RAY DIFFRACTION99.8641
2.155-2.2140.351340.338694X-RAY DIFFRACTION100
2.214-2.2780.307270.305667X-RAY DIFFRACTION100
2.278-2.3480.337350.29649X-RAY DIFFRACTION100
2.348-2.4250.402340.296625X-RAY DIFFRACTION99.8485
2.425-2.510.305170.282610X-RAY DIFFRACTION100
2.51-2.6040.4260.262595X-RAY DIFFRACTION100
2.604-2.710.3200.248570X-RAY DIFFRACTION100
2.71-2.830.383220.246556X-RAY DIFFRACTION100
2.83-2.9680.28230.236530X-RAY DIFFRACTION100
2.968-3.1280.367200.251497X-RAY DIFFRACTION100
3.128-3.3180.323130.25479X-RAY DIFFRACTION100
3.318-3.5460.262350.225430X-RAY DIFFRACTION100
3.546-3.8290.304280.22399X-RAY DIFFRACTION100
3.829-4.1930.36160.187385X-RAY DIFFRACTION100
4.193-4.6850.195150.15354X-RAY DIFFRACTION100
4.685-5.4040.152150.127297X-RAY DIFFRACTION100
5.404-6.6060.254130.186259X-RAY DIFFRACTION100
6.606-9.2870.204110.163207X-RAY DIFFRACTION100

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