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- PDB-8y5b: Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-h... -

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Basic information

Entry
Database: PDB / ID: 8y5b
TitleCrystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-hydroxyl-acepromazine.
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / TRIM21 / PRYSPRY / (R)-hydroxyl-acepromazine
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 / protein K48-linked ubiquitination / proteasomal protein catabolic process / Regulation of innate immune responses to cytosolic DNA / protein autoubiquitination / positive regulation of DNA-binding transcription factor activity / 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: 1.74 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: Cell / Year: 2024
Title: Selective degradation of multimeric proteins by TRIM21-based molecular glue and PROTAC degraders.
Authors: Lu, P. / Cheng, Y. / Xue, L. / Ren, X. / Xu, X. / Chen, C. / Cao, L. / Li, J. / Wu, Q. / Sun, S. / Hou, J. / Jia, W. / Wang, W. / Ma, Y. / Jiang, Z. / 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
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
Water2,648147
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)100.889, 100.889, 48.194
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-351-

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-A1D5Z / (1~{R})-1-[10-[3-(dimethylamino)propyl]phenothiazin-2-yl]ethanol


Mass: 328.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
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: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.74→48.19 Å / Num. obs: 26245 / % possible obs: 99.9 % / Redundancy: 24.9 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.016 / Rrim(I) all: 0.08 / Χ2: 1.01 / Net I/σ(I): 25.2 / Num. measured all: 653164
Reflection shellResolution: 1.74→1.77 Å / % possible obs: 97.5 % / Redundancy: 19.7 % / Rmerge(I) obs: 1.691 / Num. measured all: 27236 / Num. unique obs: 1382 / CC1/2: 0.762 / Rpim(I) all: 0.386 / Rrim(I) all: 1.736 / Χ2: 0.98 / Net I/σ(I) obs: 2.2

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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: 1.74→28.67 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2034 2000 7.64 %
Rwork0.1738 --
obs0.1761 26188 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1453 0 23 147 1623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131544
X-RAY DIFFRACTIONf_angle_d1.3362107
X-RAY DIFFRACTIONf_dihedral_angle_d6.945204
X-RAY DIFFRACTIONf_chiral_restr0.096213
X-RAY DIFFRACTIONf_plane_restr0.012272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.351380.32081669X-RAY DIFFRACTION98
1.78-1.830.30511410.26761696X-RAY DIFFRACTION100
1.83-1.880.23661400.21131694X-RAY DIFFRACTION100
1.88-1.940.20721400.18791699X-RAY DIFFRACTION100
1.94-2.010.20761410.1611717X-RAY DIFFRACTION100
2.01-2.090.21741410.16511707X-RAY DIFFRACTION100
2.09-2.190.21131420.17071705X-RAY DIFFRACTION100
2.19-2.30.20351410.1751714X-RAY DIFFRACTION100
2.3-2.450.20711420.19251716X-RAY DIFFRACTION100
2.45-2.640.22881430.19761723X-RAY DIFFRACTION100
2.64-2.90.23071430.19461732X-RAY DIFFRACTION100
2.9-3.320.22981450.17841753X-RAY DIFFRACTION100
3.32-4.180.18491480.14331784X-RAY DIFFRACTION100
4.18-28.670.16081550.15911879X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.2598 Å / Origin y: 30.2061 Å / Origin z: 3.7735 Å
111213212223313233
T0.2137 Å2-0.0244 Å20.0027 Å2-0.211 Å2-0.0181 Å2--0.228 Å2
L2.1468 °2-0.2762 °20.4 °2-2.6277 °2-0.7702 °2--1.315 °2
S0.0237 Å °0.0125 Å °-0.0965 Å °-0.1075 Å °0.0399 Å °0.0303 Å °0.1285 Å °-0.0864 Å °-0.0605 Å °
Refinement TLS groupSelection details: all

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