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- PDB-4tn3: Structure of the BBox-Coiled-coil region of Rhesus Trim5alpha -

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Basic information

Entry
Database: PDB / ID: 4tn3
TitleStructure of the BBox-Coiled-coil region of Rhesus Trim5alpha
ComponentsTRIM5/cyclophilin A fusion protein/T4 Lysozyme chimera
KeywordsANTIVIRAL PROTEIN / Trim protein Coiled-coil scaffold retroviral restriction factor
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / peptidyl-prolyl cis-trans isomerase activity / autophagy / ubiquitin-protein transferase activity / cell wall macromolecule catabolic process / protein folding / lysozyme / lysozyme activity / defense response to virus ...viral release from host cell by cytolysis / peptidoglycan catabolic process / peptidyl-prolyl cis-trans isomerase activity / autophagy / ubiquitin-protein transferase activity / cell wall macromolecule catabolic process / protein folding / lysozyme / lysozyme activity / defense response to virus / host cell cytoplasm / defense response to bacterium / innate immune response / zinc ion binding / cytoplasm
Similarity search - Function
Tripartite motif-containing protein 5 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Classic Zinc Finger / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. ...Tripartite motif-containing protein 5 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Classic Zinc Finger / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Lysozyme - #40 / Double Stranded RNA Binding Domain / Endolysin T4 type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Lysozyme / Lysozyme-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase TRIM5 / Endolysin
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1989 Å
AuthorsKirkpatrick, J.J. / Stoye, J.P. / Taylor, I.A. / Goldstone, D.C.
Funding support New Zealand, United Kingdom, 2items
OrganizationGrant numberCountry
NZ GovernmentRDF-UOA1102 New Zealand
Medical Research Council (MRC, United Kingdom)U117565647 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural studies of postentry restriction factors reveal antiparallel dimers that enable avid binding to the HIV-1 capsid lattice.
Authors: Goldstone, D.C. / Walker, P.A. / Calder, L.J. / Coombs, P.J. / Kirkpatrick, J. / Ball, N.J. / Hilditch, L. / Yap, M.W. / Rosenthal, P.B. / Stoye, J.P. / Taylor, I.A.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIM5/cyclophilin A fusion protein/T4 Lysozyme chimera
B: TRIM5/cyclophilin A fusion protein/T4 Lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9316
Polymers92,6702
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-92 kcal/mol
Surface area41510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.118, 59.745, 146.962
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number5
Space group name H-MC121
DetailsDimer confirmed by size exclusion chromatography

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Components

#1: Protein TRIM5/cyclophilin A fusion protein/T4 Lysozyme chimera / Lysis protein / Lysozyme / Muramidase


Mass: 46334.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: TRIMCyp / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G9MAP5, UniProt: P00720, lysozyme
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% PEG4000, 20% Glycerol, 0.2M monosaccharides, 0.1M Bis/Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1989→35 Å / Num. obs: 17873 / % possible obs: 98.9 % / Redundancy: 7.6 % / Net I/σ(I): 11.9
Reflection shellResolution: 3.1989→3.3 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.4 / % possible all: 95.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LYD

1lyd


Resolution: 3.1989→33.934 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 38.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3156 1724 5.02 %
Rwork0.2579 --
obs0.2609 34367 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1989→33.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 4 0 5800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075898
X-RAY DIFFRACTIONf_angle_d0.6857911
X-RAY DIFFRACTIONf_dihedral_angle_d14.0342249
X-RAY DIFFRACTIONf_chiral_restr0.027877
X-RAY DIFFRACTIONf_plane_restr0.0021026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1989-3.2930.39821340.39432638X-RAY DIFFRACTION94
3.293-3.39920.3821670.35182666X-RAY DIFFRACTION99
3.3992-3.52060.38131430.34462755X-RAY DIFFRACTION99
3.5206-3.66130.38231320.33662730X-RAY DIFFRACTION99
3.6613-3.82780.3581230.31312759X-RAY DIFFRACTION99
3.8278-4.02930.36241380.27292755X-RAY DIFFRACTION99
4.0293-4.28130.28931600.24952701X-RAY DIFFRACTION99
4.2813-4.61110.29861540.22752736X-RAY DIFFRACTION99
4.6111-5.07370.35661450.2232694X-RAY DIFFRACTION99
5.0737-5.80470.30871260.24222757X-RAY DIFFRACTION100
5.8047-7.30140.33551370.26342739X-RAY DIFFRACTION100
7.3014-33.93560.23881650.18982713X-RAY DIFFRACTION99

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