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- PDB-8y59: Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-h... -

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Basic information

Entry
Database: PDB / ID: 8y59
TitleCrystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-hydroxyl-acepromazine.
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / PRYSPRY / (S)-hydroxyl-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 / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / STING mediated induction of host immune responses / protein K6-linked ubiquitination / 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 / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / STING mediated induction of host immune responses / protein K6-linked ubiquitination / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / protein monoubiquitination / response to type II interferon / protein K63-linked ubiquitination / protein autoubiquitination / proteasomal protein catabolic process / protein K48-linked ubiquitination / positive regulation of autophagy / positive regulation of cell cycle / negative regulation of innate immune response / autophagosome / Regulation of innate immune responses to cytosolic DNA / positive regulation of DNA-binding transcription factor activity / P-body / RING-type E3 ubiquitin transferase / protein destabilization / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 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: 1.89 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,9262
Polymers21,5971
Non-polymers3281
Water1,964109
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)100.908, 100.908, 49.955
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-426-

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-A1D5Y / (1~{S})-1-[10-[3-(dimethylamino)propyl]phenothiazin-2-yl]ethanol


Mass: 328.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H24N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
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: BL17UM / Wavelength: 0.979168 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979168 Å / Relative weight: 1
ReflectionResolution: 1.89→45.13 Å / Num. obs: 21202 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.024 / Rrim(I) all: 0.094 / Χ2: 1.03 / Net I/σ(I): 16.2 / Num. measured all: 306302
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.949 / Num. unique obs: 1345 / CC1/2: 0.848 / Rpim(I) all: 0.342 / Rrim(I) all: 1 / Χ2: 1.08

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimless0.7.7data scaling
PHASER2.8.3phasing
XDSVERSION Jan 10, 2022data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→45.13 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 1998 9.45 %
Rwork0.1861 --
obs0.1907 21143 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 23 110 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131538
X-RAY DIFFRACTIONf_angle_d1.2492098
X-RAY DIFFRACTIONf_dihedral_angle_d6.782203
X-RAY DIFFRACTIONf_chiral_restr0.078212
X-RAY DIFFRACTIONf_plane_restr0.012271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.35011400.29181341X-RAY DIFFRACTION100
1.94-1.990.32781400.24211337X-RAY DIFFRACTION100
1.99-2.050.2491380.2111344X-RAY DIFFRACTION100
2.05-2.120.25951400.19221331X-RAY DIFFRACTION100
2.12-2.190.25261400.19571353X-RAY DIFFRACTION100
2.19-2.280.25081400.18911340X-RAY DIFFRACTION100
2.28-2.380.25431430.19061353X-RAY DIFFRACTION100
2.38-2.510.27691410.20431362X-RAY DIFFRACTION100
2.51-2.670.27981410.21671352X-RAY DIFFRACTION100
2.67-2.870.2781430.22891362X-RAY DIFFRACTION100
2.87-3.160.25751440.20811379X-RAY DIFFRACTION100
3.16-3.620.22641450.1831387X-RAY DIFFRACTION100
3.62-4.560.1671470.14051404X-RAY DIFFRACTION100
4.56-45.130.22351560.17471500X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.14 Å / Origin y: 29.9297 Å / Origin z: 4.4477 Å
111213212223313233
T0.2317 Å2-0.0166 Å20.005 Å2-0.2417 Å2-0.0299 Å2--0.3605 Å2
L2.3004 °2-0.5635 °20.6285 °2-2.9024 °2-1.0305 °2--1.8814 °2
S0.0173 Å °-0.0179 Å °0.0108 Å °-0.1425 Å °0.0146 Å °-0.0239 Å °0.1408 Å °-0.0383 Å °-0.0309 Å °
Refinement TLS groupSelection details: all

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