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- PDB-9ek5: TRIM21 PrySpry domain bound to an enhanced PRLX-93936 analog -

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Basic information

Entry
Database: PDB / ID: 9ek5
TitleTRIM21 PrySpry domain bound to an enhanced PRLX-93936 analog
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsIMMUNE SYSTEM / TRIM21 / ubiquitin / ubiquitin ligase / small molecule / protein degradation / innate immunity / cancer / therapeutics
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 / negative regulation of NF-kappaB transcription factor activity / stress granule disassembly ...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 / negative regulation of NF-kappaB transcription factor activity / stress granule disassembly / pyroptotic inflammatory response / protein K63-linked ubiquitination / response to type II interferon / protein monoubiquitination / positive regulation of protein binding / positive regulation of DNA-binding transcription factor activity / protein K48-linked ubiquitination / proteasomal protein catabolic process / Regulation of innate immune responses to cytosolic DNA / protein autoubiquitination / positive regulation of cell cycle / positive regulation of autophagy / antiviral innate immune response / autophagosome / negative regulation of innate immune response / P-body / protein destabilization / RING-type E3 ubiquitin transferase / KEAP1-NFE2L2 pathway / protein polyubiquitination / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / 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: 2.1 Å
AuthorsHinshaw, S.M. / Corsello, S.M. / Yuan, L. / Lu, J. / Martinez, M. / Gray, N.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: TRIM21 PrySpry domain bound to an enhanced PRLX-93936 analog
Authors: Hinshaw, S.M. / Corsello, S.M. / Yuan, L. / Lu, J. / Martinez, M. / Gray, N.S.
History
DepositionNov 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 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)20,9232
Polymers20,5061
Non-polymers4171
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.317, 99.317, 50.403
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: 20505.984 Da / Num. of mol.: 1 / Fragment: PrySpry domain
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-A1BLD / (3P)-3-(4-chloro-2-ethoxyphenyl)-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-4(3H)-one


Mass: 416.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22ClFN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 4.2 M Sodium Formate; 100 mM Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: the upper/lower limit were set to 120K/80K
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.84→99.32 Å / Num. obs: 22542 / % possible obs: 99.8 % / Redundancy: 26.1 % / CC1/2: 0.998 / Net I/σ(I): 7.4
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1015 / CC1/2: 0.344 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→70.326 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.944 / SU B: 15.247 / SU ML: 0.308 / Cross valid method: FREE R-VALUE / ESU R: 0.193 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2647 731 5.067 %
Rwork0.1953 13697 -
all0.199 --
obs-14428 94.753 %
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: 62.801 Å2
Baniso -1Baniso -2Baniso -3
1--3.012 Å2-0 Å2-0 Å2
2---3.012 Å20 Å2
3---6.024 Å2
Refinement stepCycle: LAST / Resolution: 2.1→70.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 29 71 1549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121530
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161353
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.7952086
X-RAY DIFFRACTIONr_angle_other_deg0.5171.7473124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4915180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.912610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50810225
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.881073
X-RAY DIFFRACTIONr_chiral_restr0.0730.2210
X-RAY DIFFRACTIONr_chiral_restr_other0.0320.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined0.2080.2277
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21294
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2750
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2800
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.26
X-RAY DIFFRACTIONr_nbd_other0.2120.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.24
X-RAY DIFFRACTIONr_mcbond_it5.4496.347723
X-RAY DIFFRACTIONr_mcbond_other5.3856.35723
X-RAY DIFFRACTIONr_mcangle_it8.06711.404902
X-RAY DIFFRACTIONr_mcangle_other8.06611.407903
X-RAY DIFFRACTIONr_scbond_it6.3746.78807
X-RAY DIFFRACTIONr_scbond_other6.3716.777808
X-RAY DIFFRACTIONr_scangle_it9.9812.1511184
X-RAY DIFFRACTIONr_scangle_other9.97612.1461185
X-RAY DIFFRACTIONr_lrange_it13.93476.6476256
X-RAY DIFFRACTIONr_lrange_other13.93376.6416257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.484220.495050.4910780.5750.56848.88680.481
2.154-2.2130.54400.4547940.45810780.6970.68877.36550.448
2.213-2.2780.421480.4499990.44810490.7880.73799.80930.443
2.278-2.3480.39540.4119480.4110020.8490.7931000.401
2.348-2.4250.358470.3979560.39510030.8120.7971000.384
2.425-2.5090.401520.3878950.3889470.7910.8041000.367
2.509-2.6040.373530.3658660.3669200.8610.8299.89130.347
2.604-2.710.444300.3128730.3179030.7580.8781000.277
2.71-2.8310.322430.2748140.2778570.9170.9181000.234
2.831-2.9690.286450.2287810.2328260.9410.9521000.184
2.969-3.1290.257490.2067330.217820.9540.9641000.178
3.129-3.3180.344450.1867040.1957490.9170.9751000.159
3.318-3.5470.295370.186640.1867010.9550.9761000.152
3.547-3.830.226330.1556350.1596680.9660.9831000.133
3.83-4.1940.248330.1445720.156050.9620.9861000.12
4.194-4.6870.188250.1115350.1155600.9790.9911000.094
4.687-5.4090.153270.1064710.1094980.9840.9921000.089
5.409-6.6140.236240.1264070.1314310.9660.9911000.104
6.614-9.3130.166150.1323330.1343480.9840.9891000.115
9.313-70.3260.25790.1882100.1912190.950.9771000.175

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