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- PDB-2lm3: Structure of the rhesus monkey TRIM5alpha PRYSPRY domain -

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Basic information

Entry
Database: PDB / ID: 2lm3
TitleStructure of the rhesus monkey TRIM5alpha PRYSPRY domain
ComponentsTripartite motif-containing protein 5
KeywordsLIGASE
Function / homology
Function and homology information


regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / pattern recognition receptor activity / negative regulation of viral genome replication / protein K63-linked ubiquitination / positive regulation of autophagy / activation of innate immune response ...regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / pattern recognition receptor activity / negative regulation of viral genome replication / protein K63-linked ubiquitination / positive regulation of autophagy / activation of innate immune response / positive regulation of DNA-binding transcription factor activity / P-body / RING-type E3 ubiquitin transferase / autophagy / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
SPRY domain / Zinc finger, RING-type, eukaryotic / : / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain ...SPRY domain / Zinc finger, RING-type, eukaryotic / : / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / 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
Tripartite motif-containing protein 5
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBiris, N. / Yang, Y. / Taylor, A.B. / Tomashevski, A. / Guo, M. / Hart, P.J. / Diaz-Griffero, F. / Ivanov, D.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the rhesus monkey TRIM5alpha PRYSPRY domain, the HIV capsid recognition module.
Authors: Biris, N. / Yang, Y. / Taylor, A.B. / Tomashevski, A. / Guo, M. / Hart, P.J. / Diaz-Griffero, F. / Ivanov, D.N.
History
DepositionNov 21, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Tripartite motif-containing protein 5


Theoretical massNumber of molelcules
Total (without water)23,3611
Polymers23,3611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tripartite motif-containing protein 5 / TRIM5alpha


Mass: 23361.430 Da / Num. of mol.: 1 / Fragment: SPRY domain residues 292-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TRIM5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0PF16, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1333D HNCO
1433D HNCA
1533D HN(CO)CA
1633D HN(CA)CB
1733D HN(COCA)CB
1813D 1H-15N NOESY
1933D H(CCO)NH
11033D C(CO)NH
11123D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1250 mM [U-98% 15N] SPRY, 93% H2O/7% D2O93% H2O/7% D2O
2250 mM [U-99% 13C; U-99% 15N] SPRY, 93% H2O/7% D2O93% H2O/7% D2O
3250 mM [U-13C; U-15N; U-2H] SPRY, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 mMSPRY-1[U-98% 15N]1
250 mMSPRY-2[U-99% 13C; U-99% 15N]2
250 mMSPRY-3[U-13C; U-15N; U-2H]3
Sample conditionsIonic strength: 0.05 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE WHOLE PROTEIN WAS ASSIGNED BY NMR. THE FINAL STRUCTURES OF THE PROTEIN WERE CALCULATED USING XPLOR-NIH. SIMULATED ANNEALING WITH NOE-DERIVED DISTANCE RESTRAINTS WAS APPLIED TO THE 325- ...Details: THE WHOLE PROTEIN WAS ASSIGNED BY NMR. THE FINAL STRUCTURES OF THE PROTEIN WERE CALCULATED USING XPLOR-NIH. SIMULATED ANNEALING WITH NOE-DERIVED DISTANCE RESTRAINTS WAS APPLIED TO THE 325-349 LOOP ONLY WHEREAS RESIDUES 291-324 WERE HELD FIXED AT THE COORDINATES DETERMINED BY X-RAY CRYSTALLOGRAPHY FROM PDB ENTRY 3UV9.
NMR constraintsNOE constraints total: 259 / NOE intraresidue total count: 103 / NOE long range total count: 5 / NOE medium range total count: 49 / NOE sequential total count: 102
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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