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- PDB-5olm: TRIM21 -

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Basic information

Entry
Database: PDB / ID: 5olm
TitleTRIM21
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsANTIVIRAL PROTEIN / antibody
Function / homology
Function and homology information


negative regulation of protein deubiquitination / regulation of viral entry into host cell / protein K27-linked ubiquitination / suppression of viral release by host / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / stress granule disassembly ...negative regulation of protein deubiquitination / regulation of viral entry into host cell / protein K27-linked ubiquitination / suppression of viral release by host / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / 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 / autophagosome / proteasomal protein catabolic process / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of autophagy / positive regulation of cell cycle / Regulation of innate immune responses to cytosolic DNA / negative regulation of innate immune response / P-body / protein destabilization / RING-type E3 ubiquitin transferase / positive regulation of DNA-binding transcription factor activity / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / Interferon gamma signaling / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein binding / 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 / cell cycle / innate immune response / protein kinase binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / zinc finger of C3HC4-type, RING / 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 / zinc finger of C3HC4-type, RING / 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. / Classic Zinc Finger / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Double Stranded RNA Binding 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJames, L.C.
CitationJournal: Elife / Year: 2018
Title: Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21.
Authors: Dickson, C. / Fletcher, A. / Vaysburd, M. / Yang, J.C. / Mallery, D.L. / Zeng, J. / Johnson, C.M. / McLaughlin, S.H. / Skehel, M. / Maslen, S. / Cruickshank, J. / Huguenin-Dezot, N. / Chin, ...Authors: Dickson, C. / Fletcher, A. / Vaysburd, M. / Yang, J.C. / Mallery, D.L. / Zeng, J. / Johnson, C.M. / McLaughlin, S.H. / Skehel, M. / Maslen, S. / Cruickshank, J. / Huguenin-Dezot, N. / Chin, J.W. / Neuhaus, D. / James, L.C.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,10210
Polymers29,5782
Non-polymers5238
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-12 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.400, 83.260, 117.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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 / RING- ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / RING-type E3 ubiquitin transferase TRIM21 / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 14789.140 Da / Num. of mol.: 2
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 300 K / Method: batch mode / Details: na

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→67.95 Å / Num. obs: 21198 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.9
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→67.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.324 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26162 1025 4.9 %RANDOM
Rwork0.20833 ---
obs0.21087 19875 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.875 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å20 Å20 Å2
2---0.74 Å20 Å2
3----1.87 Å2
Refinement stepCycle: 1 / Resolution: 1.95→67.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 8 37 2024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192047
X-RAY DIFFRACTIONr_bond_other_d0.0030.021864
X-RAY DIFFRACTIONr_angle_refined_deg2.0791.9622752
X-RAY DIFFRACTIONr_angle_other_deg1.1363.014300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7545253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83823.47892
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13715355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7431518
X-RAY DIFFRACTIONr_chiral_restr0.1250.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212249
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4543.8611024
X-RAY DIFFRACTIONr_mcbond_other3.453.8611023
X-RAY DIFFRACTIONr_mcangle_it4.4035.7621273
X-RAY DIFFRACTIONr_mcangle_other4.4035.7621274
X-RAY DIFFRACTIONr_scbond_it4.6184.2041023
X-RAY DIFFRACTIONr_scbond_other4.6194.2041020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5246.1291478
X-RAY DIFFRACTIONr_long_range_B_refined7.57345.6642184
X-RAY DIFFRACTIONr_long_range_B_other7.57445.6422180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 75 -
Rwork0.367 1447 -
obs--99.15 %

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