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- PDB-3uv9: Structure of the rhesus monkey TRIM5alpha deltav1 PRYSPRY domain -

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Basic information

Entry
Database: PDB / ID: 3uv9
TitleStructure of the rhesus monkey TRIM5alpha deltav1 PRYSPRY domain
ComponentsTripartite motif-containing protein 5
KeywordsLIGASE / domain swap / antiretroviral / HIV Capsid
Function / homology
Function and homology information


regulation of viral entry into host cell / suppression of viral release by host / regulation of lipopolysaccharide-mediated signaling pathway / 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 / suppression of viral release by host / regulation of lipopolysaccharide-mediated signaling pathway / 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 / P-body / RING-type E3 ubiquitin transferase / autophagy / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / 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 / B30.2/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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 Å
AuthorsBiris, N. / Yang, Y. / Taylor, A.B. / Tomashevskii, A. / Guo, M. / Hart, P.J. / Diaz-Griffero, F. / Ivanov, D.
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 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 5


Theoretical massNumber of molelcules
Total (without water)20,7391
Polymers20,7391
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tripartite motif-containing protein 5

A: Tripartite motif-containing protein 5

A: Tripartite motif-containing protein 5


Theoretical massNumber of molelcules
Total (without water)62,2183
Polymers62,2183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9880 Å2
ΔGint-64 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.570, 86.570, 77.338
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsMONOMERIC, UNSWAPPED

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Components

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


Mass: 20739.434 Da / Num. of mol.: 1 / Fragment: SPRY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TRIM5 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2
References: UniProt: Q0PF16, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT RESIDUES 326-349 WERE DELETED AND WERE REPLACED WITH AN ALA-GLY LINKER.

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.17 M magnesium formate, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 31006 / % possible obs: 98.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.044 / Net I/σ(I): 31.4
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 3089 / Rsym value: 0.456 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WL1

2wl1


Resolution: 1.549→26.915 Å / SU ML: 0.18 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1939 6.5 %random
Rwork0.1478 ---
obs0.151 29851 95.02 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.457 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.017 Å20 Å20 Å2
2--3.017 Å20 Å2
3----2.1911 Å2
Refinement stepCycle: LAST / Resolution: 1.549→26.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 0 155 1600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051507
X-RAY DIFFRACTIONf_angle_d0.9492057
X-RAY DIFFRACTIONf_dihedral_angle_d11.618537
X-RAY DIFFRACTIONf_chiral_restr0.07224
X-RAY DIFFRACTIONf_plane_restr0.003263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5491-1.58780.29451230.21271812X-RAY DIFFRACTION87
1.5878-1.63070.27261240.2031905X-RAY DIFFRACTION90
1.6307-1.67870.23571310.15881877X-RAY DIFFRACTION90
1.6787-1.73290.22661400.15111953X-RAY DIFFRACTION92
1.7329-1.79480.22591400.13851970X-RAY DIFFRACTION93
1.7948-1.86670.22121380.13191960X-RAY DIFFRACTION95
1.8667-1.95160.20181440.12452023X-RAY DIFFRACTION96
1.9516-2.05440.19561430.13152054X-RAY DIFFRACTION98
2.0544-2.18310.17821400.12972071X-RAY DIFFRACTION99
2.1831-2.35160.19191430.12452068X-RAY DIFFRACTION99
2.3516-2.58810.1811470.14832097X-RAY DIFFRACTION100
2.5881-2.96210.18451450.1532102X-RAY DIFFRACTION100
2.9621-3.73040.18331460.14322092X-RAY DIFFRACTION100
3.7304-26.91910.19741350.16421928X-RAY DIFFRACTION92

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