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- PDB-7hny: PanDDA analysis group deposition -- Crystal Structure of TRIM21 i... -

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Basic information

Entry
Database: PDB / ID: 7hny
TitlePanDDA analysis group deposition -- Crystal Structure of TRIM21 in complex with Z44592329
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsLIGASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / TRIM21
Function / homology
Function and homology information


negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / regulation of viral entry into host cell / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity / response to type II interferon / protein monoubiquitination / protein K63-linked ubiquitination ...negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / regulation of viral entry into host cell / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / stress granule disassembly / negative regulation of NF-kappaB transcription factor activity / response to type II interferon / protein monoubiquitination / protein K63-linked ubiquitination / protein autoubiquitination / positive regulation of autophagy / positive regulation of cell cycle / negative regulation of innate immune response / autophagosome / P-body / protein destabilization / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of protein binding / regulation of protein localization / cytoplasmic vesicle / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ribonucleoprotein complex / innate immune response / protein kinase binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / 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 / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / 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
N-phenyl-N'-pyridin-3-ylurea / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.28 Å
AuthorsKim, Y. / Marples, P. / Fearon, D. / von Delft, F. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)875510European Union
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Kim, Y. / Marples, P. / Fearon, D. / von Delft, F. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionNov 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,0305
Polymers21,5961
Non-polymers4334
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.342, 95.342, 45.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-431-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM21 / 52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / Ro(SS-A) / Sjoegren syndrome ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 21596.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim21, Ro52, Ssa1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q62191, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-K0G / N-phenyl-N'-pyridin-3-ylurea


Mass: 213.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.41 Å3/Da / Density % sol: 48.87 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4 % PEG 400, 2 M AmmSO4, 0.1 M HEPES pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92134 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92134 Å / Relative weight: 1
ReflectionResolution: 1.28→41.23 Å / Num. obs: 52395 / % possible obs: 98.8 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.023 / Rrim(I) all: 0.081 / Net I/σ(I): 16.5 / Num. measured all: 568711 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.28-1.33.41.256760222660.340.7931.50.586
7.01-41.2312.20.05242933510.9950.0170.05595.699.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.28→41.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.069 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 2549 4.9 %RANDOM
Rwork0.1778 ---
obs0.1785 49818 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.19 Å2 / Biso mean: 16.634 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å20 Å2
2--0.07 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.28→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 29 143 1665
Biso mean--37.69 27.16 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151626
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.642553
X-RAY DIFFRACTIONr_angle_other_deg1.4591.583750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2215241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.16621.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6061515
X-RAY DIFFRACTIONr_chiral_restr0.0870.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022308
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02520
X-RAY DIFFRACTIONr_mcbond_it1.3931.459972
X-RAY DIFFRACTIONr_mcbond_other1.3611.435965
X-RAY DIFFRACTIONr_mcangle_it2.1842.161153
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 204 -
Rwork0.355 3238 -
all-3442 -
obs--87.72 %

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