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- PDB-5jpx: Solution structure of the TRIM21 B-box2 (B2) -

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Basic information

Entry
Database: PDB / ID: 5jpx
TitleSolution structure of the TRIM21 B-box2 (B2)
ComponentsE3 ubiquitin-protein ligase TRIM21
KeywordsMETAL BINDING PROTEIN / B-box / RING-like fold / E3 ligase / TRIM protein / Zinc-binding motif / Ubiquitination
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 / 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 ...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. / 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. / 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)
MethodSOLUTION NMR / simulated annealing
AuthorsWallenhammar, A. / Anandapadamanaban, M. / Sunnerhagen, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Cancerfonden Sweden
CitationJournal: PLoS ONE / Year: 2017
Title: Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain.
Authors: Wallenhammar, A. / Anandapadamanaban, M. / Lemak, A. / Mirabello, C. / Lundstrom, P. / Wallner, B. / Sunnerhagen, M.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 7, 2018Group: Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.0Oct 30, 2019Group: Atomic model / Data collection / Database references
Category: atom_site / pdbx_database_related / pdbx_nmr_spectrometer
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2092
Polymers5,1441
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 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: 5143.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli)
References: UniProt: P19474, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D HN(CO)CA
161isotropic13D H(CCO)NH
171isotropic13D CBCA(CO)NH
181isotropic13D 1H-15N TOCSY
191isotropic13D 1H-15N NOESY
2102isotropic22D 1H-13C HSQC aliphatic
2112isotropic22D 1H-13C HSQC aromatic
2122isotropic23D (H)CCH-TOCSY
2132isotropic23D 1H-13C NOESY aliphatic
2142isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1450 uM [U-13C; U-15N] TRIM21 Bbox2, 50 mM TRIS, 150 mM sodium chloride, 10 mM beta-mercaptoethanol, 10 uM ZINC ION, 10 % glycerol, 90% H2O/10% D2O13C, 15N-Bbox2 for backbone assignmentBackbone_assignment90% H2O/10% D2O
solution2450 uM [U-13C; U-15N] TRIM21 Bbox2, 50 mM deuterated TRIS, 150 mM sodium chloride, 10 mM beta-mercaptoethanol, 10 uM ZINC ION, 10 % glycerol, 90% H2O/10% D2O13C, 15N-Bbox2 for sidechain assignmentSidechain_assignment90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMTRIM21 Bbox2[U-13C; U-15N]1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
10 mMbeta-mercaptoethanolnatural abundance1
10 uMZINC IONnatural abundance1
10 %glycerolnatural abundance1
450 uMTRIM21 Bbox2[U-13C; U-15N]2
50 mMTRISdeuterated2
150 mMsodium chloridenatural abundance2
10 mMbeta-mercaptoethanolnatural abundance2
10 uMZINC IONnatural abundance2
10 %glycerolnatural abundance2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
150mM TRIS, 150mM NaCl, 10mM Betamercaptoethanol, 10uM ZnCl250mM TRIS, 150mM NaCl mMBackbone_assignment7.5 Ambient bar298 K
250mM TRIS, 150mM NaCl, 10mM Betamercaptoethanol, 10uM ZnCl250mM TRIS, 150mM NaCl mMSidechain_assignment7.5 Ambient bar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA6001Backbone
Bruker AVANCE IIIBrukerAVANCE III8002Sidechain

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TALOSCornilescu, Delaglio and Baxstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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