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- PDB-8y58: Crystal structure of TRIM21 PRYSPRY (D355A) in complex with acepr... -

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Basic information

Entry
Database: PDB / ID: 8y58
TitleCrystal structure of TRIM21 PRYSPRY (D355A) in complex with acepromazine.
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / PRYSPRY / acepromazine
Function / homology
Function and homology information


negative regulation of protein deubiquitination / regulation of viral entry into host cell / suppression of viral release by host / protein K27-linked ubiquitination / STING mediated induction of host immune responses / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / cellular response to chemical stress / stress granule disassembly ...negative regulation of protein deubiquitination / regulation of viral entry into host cell / suppression of viral release by host / protein K27-linked ubiquitination / STING mediated induction of host immune responses / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / cellular response to chemical stress / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / response to type II interferon / protein monoubiquitination / protein K63-linked ubiquitination / positive regulation of cell cycle / protein autoubiquitination / proteasomal protein catabolic process / protein K48-linked ubiquitination / positive regulation of autophagy / negative regulation of innate immune response / autophagosome / Regulation of innate immune responses to cytosolic DNA / positive regulation of DNA-binding transcription factor activity / protein destabilization / P-body / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / Interferon gamma signaling / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein binding / regulation of protein localization / cytoplasmic vesicle / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / positive regulation of viral entry into host cell / protein ubiquitination / ribonucleoprotein complex / innate immune response / protein kinase binding / protein homodimerization activity / 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 / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Modified RING finger domain / U-box domain / B-box zinc finger ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Modified RING finger domain / U-box 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
FORMIC ACID / Chem-PMZ / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLu, P. / Cheng, Y. / Xue, L. / Ren, X. / Huang, N. / Han, T.
Funding support China, 2items
OrganizationGrant numberCountry
Other governmentZ201100005320010 China
Other governmentZ221100007022004 China
CitationJournal: To be published
Title: Selective degradation of multimeric proteins via chemically induced proximity to TRIM21.
Authors: Lu, P. / Cheng, Y. / Xue, L. / Ren, X. / Chen, C. / Li, J. / Wu, Q. / Sun, S. / Hou, J. / Jia, W. / Li, C. / Qi, X. / Huang, N. / Han, T.
History
DepositionJan 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0625
Polymers21,5971
Non-polymers4654
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.415, 100.415, 49.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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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: 21597.229 Da / Num. of mol.: 1 / Mutation: D355A
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-PMZ / 1-[10-(3-DIMETHYLAMINO-PROPYL)-10H-PHENOTHIAZIN-2-YL]-ETHANONE / ACETYLPROMAZINE


Mass: 326.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2OS / Feature type: SUBJECT OF INVESTIGATION / Comment: antipsychotic*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris (pH 7.0), 3.5 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979145 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979145 Å / Relative weight: 1
ReflectionResolution: 1.6→44.91 Å / Num. obs: 33072 / % possible obs: 97.5 % / Redundancy: 14.2 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.014 / Rrim(I) all: 0.054 / Χ2: 1.06 / Net I/σ(I): 24.5 / Num. measured all: 470044
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 99.2 % / Redundancy: 14.4 % / Rmerge(I) obs: 1.404 / Num. measured all: 22991 / Num. unique obs: 1595 / CC1/2: 0.856 / Rpim(I) all: 0.381 / Rrim(I) all: 1.456 / Χ2: 0.96 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimless0.7.7data scaling
XDSVERSION Jan 10, 2022data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.83 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 1997 6.06 %
Rwork0.1762 --
obs0.1778 32950 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 32 126 1607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151543
X-RAY DIFFRACTIONf_angle_d1.4362101
X-RAY DIFFRACTIONf_dihedral_angle_d7.738205
X-RAY DIFFRACTIONf_chiral_restr0.099212
X-RAY DIFFRACTIONf_plane_restr0.013271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.31121420.27152198X-RAY DIFFRACTION99
1.64-1.680.28411430.23922217X-RAY DIFFRACTION100
1.68-1.730.25251440.22732232X-RAY DIFFRACTION100
1.73-1.790.28091440.21192244X-RAY DIFFRACTION100
1.79-1.850.20161450.18582248X-RAY DIFFRACTION100
1.85-1.930.21571430.21352227X-RAY DIFFRACTION99
1.93-2.020.20431450.17212233X-RAY DIFFRACTION100
2.02-2.120.22321450.18252230X-RAY DIFFRACTION99
2.12-2.250.19061460.17582270X-RAY DIFFRACTION100
2.26-2.430.21741460.1812272X-RAY DIFFRACTION100
2.43-2.640.21481300.18292014X-RAY DIFFRACTION100
2.7-3.060.19961340.18982085X-RAY DIFFRACTION100
3.06-3.850.16841390.16812143X-RAY DIFFRACTION92
3.85-28.830.19721510.1532340X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -11.0809 Å / Origin y: 29.8475 Å / Origin z: 4.0921 Å
111213212223313233
T0.2068 Å2-0.0118 Å20.0212 Å2-0.2063 Å2-0.018 Å2--0.1729 Å2
L2.0334 °2-0.2166 °20.4002 °2-2.2753 °2-0.5618 °2--1.2307 °2
S0.002 Å °-0.0331 Å °-0.0747 Å °-0.1145 Å °0.0167 Å °-0.0008 Å °0.0886 Å °-0.0576 Å °-0.0169 Å °
Refinement TLS groupSelection details: all

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