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- PDB-5hgo: Hexameric HIV-1 CA R18G mutant -

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Basic information

Entry
Database: PDB / ID: 5hgo
TitleHexameric HIV-1 CA R18G 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) / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1.0Aug 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)25,3611
Polymers25,3611
Non-polymers00
Water1,892105
1
A: Capsid protein P24
x 6


Theoretical massNumber of molelcules
Total (without water)152,1676
Polymers152,1676
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 area13280 Å2
ΔGint-110 kcal/mol
Surface area58790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.810, 90.810, 56.880
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: 25361.129 Da / Num. of mol.: 1 / Mutation: C14A, C45E, A184W, A185M, R18G
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.: 105 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.878
11K, H, -L20.122
ReflectionResolution: 2→46.09 Å / Num. obs: 18210 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.073 / Net I/σ(I): 6.5 / Num. measured all: 109659 / Scaling rejects: 160
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
2-2.055.90.8311.9783813300.6640.374100
8.94-46.095.50.10212.711732120.9910.04596.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.21 Å39.32 Å
Translation5.21 Å39.32 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
Aimless0.5.12data scaling
PHASER2.5.7phasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4E

3h4e


Resolution: 2→39.32 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2175 / WRfactor Rwork: 0.2046 / FOM work R set: 0.8615 / SU B: 4.572 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0358 / SU Rfree: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 921 5.1 %RANDOM
Rwork0.2051 ---
obs0.206 17285 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.41 Å2 / Biso mean: 27.327 Å2 / Biso min: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1-6.07 Å20 Å20 Å2
2--6.07 Å20 Å2
3----12.13 Å2
Refinement stepCycle: final / Resolution: 2→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 0 105 1678
Biso mean---28.57 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191644
X-RAY DIFFRACTIONr_bond_other_d0.0010.021578
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.9622240
X-RAY DIFFRACTIONr_angle_other_deg0.8763.0013638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9825212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21524.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27615282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.231510
X-RAY DIFFRACTIONr_chiral_restr0.0590.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_mcbond_it1.3872.752833
X-RAY DIFFRACTIONr_mcbond_other1.3882.749832
X-RAY DIFFRACTIONr_mcangle_it2.2194.6151041
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 80 -
Rwork0.216 1246 -
all-1326 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36480.0575-0.07460.6326-0.3941.04060.01730.0416-0.0152-0.0679-0.03570.00310.04010.08820.01840.00880.0068-0.00210.014-0.00330.087569.4238-87.1167-12.2837
22.27810.79510.35742.2559-1.03651.95190.0455-0.0949-0.1310.0925-0.0366-0.12190.1489-0.0243-0.00890.0366-0.00120.00150.00740.00530.092558.7452-113.89611.0924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 145
2X-RAY DIFFRACTION2A146 - 999

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