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- PDB-5jpa: Hexameric HIV-1 CA H12Y mutant -

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Basic information

Entry
Database: PDB / ID: 5jpa
TitleHexameric HIV-1 CA H12Y mutant
ComponentsCapsid Protein P24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsJacques, D.A. / James, L.C.
Funding support United Kingdom, Australia, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)UK; U105181010 United Kingdom
European Research Council291627 -IAI United Kingdom
National Health and Medical Research CouncilGNT1036521 Australia
CitationJournal: Nature / Year: 2016
Title: HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis.
Authors: Jacques, D.A. / McEwan, W.A. / Hilditch, L. / Price, A.J. / Towers, G.J. / James, L.C.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: 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
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: Capsid Protein P24


Theoretical massNumber of molelcules
Total (without water)25,4861
Polymers25,4861
Non-polymers00
Water2,216123
1
A: Capsid Protein P24
x 6


Theoretical massNumber of molelcules
Total (without water)152,9186
Polymers152,9186
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_435-y-1,x-y-2,z1
crystal symmetry operation3_645-x+y+1,-x-1,z1
crystal symmetry operation4_535-x,-y-2,z1
crystal symmetry operation5_655y+1,-x+y,z1
crystal symmetry operation6_445x-y-1,x-1,z1
Buried area15940 Å2
ΔGint-100 kcal/mol
Surface area59600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.600, 90.600, 56.931
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Capsid Protein P24


Mass: 25486.301 Da / Num. of mol.: 1 / Mutation: H12Y, A14C, E45C, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P12493
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 550MME (12% w/v), KSCN (0.15M), 0.1M TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→56.93 Å / Num. obs: 27756 / % possible obs: 95.1 % / Redundancy: 4.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.043 / Rrim(I) all: 0.105 / Net I/σ(I): 9 / Num. measured all: 133997 / Scaling rejects: 80
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.734.90.813194.7
9-56.935.70.063192

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.6 Å56.93 Å
Translation5.6 Å56.93 Å

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Processing

Software
NameVersionClassification
Aimless0.4.10data scaling
PHASER2.5.6phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 1.7→56.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.212 / SU ML: 0.073 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1379 5 %RANDOM
Rwork0.1971 ---
obs0.199 26370 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.18 Å2 / Biso mean: 27.491 Å2 / Biso min: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.7→56.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 0 123 1732
Biso mean---33.6 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191726
X-RAY DIFFRACTIONr_bond_other_d0.0010.021655
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.9612350
X-RAY DIFFRACTIONr_angle_other_deg0.84333813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.835220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61924.93375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.515299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2251511
X-RAY DIFFRACTIONr_chiral_restr0.060.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_mcbond_it2.1943.349871
X-RAY DIFFRACTIONr_mcbond_other2.1843.345870
X-RAY DIFFRACTIONr_mcangle_it3.4055.6131091
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 81 -
Rwork0.265 1949 -
all-2030 -
obs--93.59 %

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