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- PDB-5hgn: Hexameric HIV-1 CA, apo form -

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Basic information

Entry
Database: PDB / ID: 5hgn
TitleHexameric HIV-1 CA, apo form
ComponentsCapsid protein P24
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / 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) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsJacques, D.A. / Price, A.J. / James, D.A.
Funding support United Kingdom, Australia, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)UK; U105181010 United Kingdom
European Research Council281627 -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
DepositionJan 8, 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 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)25,4611
Polymers25,4611
Non-polymers00
Water2,234124
1
A: Capsid protein P24
x 6


Theoretical massNumber of molelcules
Total (without water)152,7686
Polymers152,7686
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_975-y+4,x-y+2,z1
crystal symmetry operation3_795-x+y+2,-x+4,z1
crystal symmetry operation4_995-x+4,-y+4,z1
crystal symmetry operation5_575y,-x+y+2,z1
crystal symmetry operation6_755x-y+2,x,z1
Buried area14270 Å2
ΔGint-105 kcal/mol
Surface area58690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.730, 90.730, 56.751
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 / Pr55Gag


Mass: 25461.271 Da / Num. of mol.: 1 / Mutation: C14A, C45E, A184W, A185M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / 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.: 124 / 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: 53.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5)

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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 / Detector: PIXEL / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→26.69 Å / Num. obs: 21070 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.059 / Net I/σ(I): 8.3 / Num. measured all: 106747 / Scaling rejects: 57
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.944.80.7482.1674814090.7290.379100
8.91-26.695.40.07417.111652150.9940.03596.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.97 Å26.69 Å
Translation4.97 Å26.69 Å

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Processing

Software
NameVersionClassification
Aimless0.4.2data scaling
PHASER2.5.7phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4E

3h4e


Resolution: 1.9→26.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2311 / WRfactor Rwork: 0.2066 / FOM work R set: 0.8514 / SU B: 3.181 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1419 / SU Rfree: 0.1275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1069 5.1 %RANDOM
Rwork0.2002 ---
obs0.2013 19999 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.25 Å2 / Biso mean: 30.171 Å2 / Biso min: 15.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å2-0 Å2
2--0.53 Å20 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 1.9→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 0 124 1704
Biso mean---35.72 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191663
X-RAY DIFFRACTIONr_bond_other_d0.0010.021601
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.9622266
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0013688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8865214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65924.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89715288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7621512
X-RAY DIFFRACTIONr_chiral_restr0.0560.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02362
X-RAY DIFFRACTIONr_mcbond_it2.3153.743838
X-RAY DIFFRACTIONr_mcbond_other2.3113.74837
X-RAY DIFFRACTIONr_mcangle_it3.4476.2841049
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 79 -
Rwork0.266 1468 -
all-1547 -
obs--99.94 %

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