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- PDB-5hgp: Hexameric HIV-1 CA in complex with hexacarboxybenzene -

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Basic information

Entry
Database: PDB / ID: 5hgp
TitleHexameric HIV-1 CA in complex with hexacarboxybenzene
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 / virion membrane / structural molecule activity / 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) / Retroviral nucleocapsid Gag protein p24, C-terminal domain ...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
BENZENE HEXACARBOXYLIC ACID / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 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 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 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 1.3Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8032
Polymers25,4611
Non-polymers3421
Water2,144119
1
A: Capsid protein P24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,82112
Polymers152,7686
Non-polymers2,0536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-y+3,x-y,z1
crystal symmetry operation3_885-x+y+3,-x+3,z1
crystal symmetry operation4_975-x+4,-y+2,z1
crystal symmetry operation5_675y+1,-x+y+2,z1
crystal symmetry operation6_645x-y+1,x-1,z1
Buried area15830 Å2
ΔGint-125 kcal/mol
Surface area59430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.759, 90.759, 56.760
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 type 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P12493
#2: Chemical ChemComp-BHC / BENZENE HEXACARBOXYLIC ACID / Mellitic acid


Mass: 342.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H6O12
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 53.59 %
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), Mellitic acid (1mM). Mellitic acid stock was adjusted to pH 8.0 with TRIS prior to setting up trays.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→45.38 Å / Num. obs: 19152 / % possible obs: 97.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Net I/σ(I): 11.7 / Num. measured all: 129940 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.95-26.50.8622.1886213570.6440.36899.5
8.94-45.386.90.04332.213661990.9990.01789.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.11 Å45.38 Å
Translation5.11 Å45.38 Å

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Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
PHASER2.5.7phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4E

3h4e


Resolution: 1.95→45.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2139 / WRfactor Rwork: 0.1834 / FOM work R set: 0.8397 / SU B: 3.668 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1533 / SU Rfree: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 964 5 %RANDOM
Rwork0.1936 ---
obs0.195 18188 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.37 Å2 / Biso mean: 31.245 Å2 / Biso min: 14.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 1.95→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 24 119 1723
Biso mean--95.41 34.09 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191675
X-RAY DIFFRACTIONr_bond_other_d0.0010.021588
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9742285
X-RAY DIFFRACTIONr_angle_other_deg0.8993.0013659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34424.49369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90915285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4541511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_mcbond_it3.9913.731833
X-RAY DIFFRACTIONr_mcbond_other3.9883.727832
X-RAY DIFFRACTIONr_mcangle_it5.1836.2631041
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 65 -
Rwork0.266 1347 -
all-1412 -
obs--99.51 %

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