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- PDB-2vok: Murine TRIM21 -

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Basic information

Entry
Database: PDB / ID: 2vok
TitleMurine TRIM21
Components52 KDA RO PROTEIN
KeywordsIMMUNE SYSTEM / POLYMORPHISM / METAL-BINDING / TRIPARTITE MOTIF (TRIM) PROTEIN / SPRY SYSTEMIC LUPUS ERYTHEMATOSUS / ZINC / B30.2 / RO.52 / NUCLEUS / PRYSPRY / CYTOPLASM / RIBONUCLEOPROTEIN / SYSTEMIC LUPUS ERYTHEMATOSUS / ZINC-FINGER / DNA-BINDING / RNA-BINDING / COILED COIL
Function / homology
Function and homology information


negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / 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 K63-linked ubiquitination / protein monoubiquitination / protein autoubiquitination ...negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / 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 K63-linked ubiquitination / protein monoubiquitination / protein autoubiquitination / positive regulation of cell cycle / positive regulation of autophagy / autophagosome / negative regulation of innate immune response / P-body / protein destabilization / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / cytoplasmic stress granule / ubiquitin protein ligase activity / positive regulation of protein binding / cytoplasmic vesicle / protein ubiquitination / ribonucleoprotein complex / DNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
SPRY domain / 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 ...SPRY domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.3 Å
AuthorsKeeble, A.H. / Khan, Z. / Forster, A. / James, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Trim21 is an Igg Receptor that is Structurally, Thermodynamically, and Kinetically Conserved.
Authors: Keeble, A.H. / Khan, Z. / Forster, A. / James, L.C.
History
DepositionFeb 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 52 KDA RO PROTEIN
B: 52 KDA RO PROTEIN


Theoretical massNumber of molelcules
Total (without water)43,0722
Polymers43,0722
Non-polymers00
Water8,665481
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-9.3 kcal/mol
Surface area20130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)62.955, 44.889, 71.794
Angle α, β, γ (deg.)90.00, 109.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 52 KDA RO PROTEIN / TRIM21 / SJOEGREN SYNDROME TYPE A ANTIGEN / SS-A / RO(SS-A) / 52 KDA RIBONUCLEOPROTEIN AUTOANTIGEN ...TRIM21 / SJOEGREN SYNDROME TYPE A ANTIGEN / SS-A / RO(SS-A) / 52 KDA RIBONUCLEOPROTEIN AUTOANTIGEN RO/SS-A / TRIPARTITE MOTIF-CONTAINING PROTEIN 21


Mass: 21536.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q62191
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 49 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1.54
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.3→29.23 Å / Num. obs: 92548 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13

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Processing

SoftwareName: REFMAC / Version: 5.3.0022 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.3→67.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.044 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4636 5.09 %RANDOM
Rwork0.214 ---
obs0.215 92549 99.6 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.498 Å20 Å20.341 Å2
2--0.685 Å20 Å2
3----0.951 Å2
Refinement stepCycle: LAST / Resolution: 1.3→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 0 481 3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213094
X-RAY DIFFRACTIONr_bond_other_d0.0040.023120
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9034207
X-RAY DIFFRACTIONr_angle_other_deg3.14537281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53223.459159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5131518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022436
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02581
X-RAY DIFFRACTIONr_nbd_refined0.2070.21417
X-RAY DIFFRACTIONr_nbd_other0.2410.33043
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22087
X-RAY DIFFRACTIONr_nbtor_other0.4470.517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2400
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.248
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.381
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.51883
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2322981
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.72831405
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.464.51226
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 5.79→67.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 47
Rwork0.255 914

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