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- PDB-5k3q: Rhesus macaques Trim5alpha Bbox2 domain -

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Basic information

Entry
Database: PDB / ID: 5k3q
TitleRhesus macaques Trim5alpha Bbox2 domain
ComponentsTripartite motif-containing protein 5,Tripartite motif-containing protein 5
KeywordsLIGASE / Zinc finger Bbox2 Antiretroviral
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
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. / Classic Zinc Finger / 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. / Classic Zinc 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 / 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
NITRATE ION / Tripartite motif-containing protein 5
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKeown, J.K. / Goldstone, D.C.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Marsden Fund New Zealand
Rutherford Fellowship New Zealand
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of the Trim5 alpha Bbox2 domain from rhesus macaques describes a plastic oligomerisation interface.
Authors: Keown, J.R. / Goldstone, D.C.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
B: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
C: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
D: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,57113
Polymers46,9864
Non-polymers5859
Water1,45981
1
A: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
B: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8177
Polymers23,4932
Non-polymers3245
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
D: Tripartite motif-containing protein 5,Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7556
Polymers23,4932
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.751, 54.556, 54.479
Angle α, β, γ (deg.)90.000, 100.030, 90.000
Int Tables number4
Space group name H-MP1211
DetailsDimer confirmed analytical ultracentrifugation

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Components

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


Mass: 11746.503 Da / Num. of mol.: 4
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)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWhile no protease is present, the authors are confident that the crystal is a fragment comprising ...While no protease is present, the authors are confident that the crystal is a fragment comprising residues 94-136 of the original construct.

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: 100 micron rectangular plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 24% (w/v) PE3350, 0.4 M LiNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2016
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→38.25 Å / Num. obs: 16550 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.847.50.9071100
9-38.256.60.052199.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.15data scaling
SHELX2006/3phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→38.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.622 / SU ML: 0.105 / SU R Cruickshank DPI: 0.2498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 873 5.3 %RANDOM
Rwork0.1774 ---
obs0.1801 15677 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.88 Å2 / Biso mean: 27.984 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-1.29 Å2
2---0.77 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 1.8→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 12 81 1450
Biso mean--32.18 35.39 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191410
X-RAY DIFFRACTIONr_bond_other_d0.0030.021283
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9121895
X-RAY DIFFRACTIONr_angle_other_deg0.8732956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8635171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57823.64974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59815251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.405158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021582
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02352
X-RAY DIFFRACTIONr_mcbond_it2.1422.684678
X-RAY DIFFRACTIONr_mcbond_other2.1282.682677
X-RAY DIFFRACTIONr_mcangle_it2.7384.012842
X-RAY DIFFRACTIONr_rigid_bond_restr2.95232693
X-RAY DIFFRACTIONr_sphericity_free33.221535
X-RAY DIFFRACTIONr_sphericity_bonded15.16252714
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 53 -
Rwork0.209 1140 -
all-1193 -
obs--100 %

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