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- PDB-5hgk: HIV-1 CA N-terminal domain, open conformation -

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Basic information

Entry
Database: PDB / ID: 5hgk
TitleHIV-1 CA N-terminal domain, open conformation
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / viral capsid / viral nucleocapsid / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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 ...Retroviral nucleocapsid Gag protein p24, N-terminal / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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
Gag protein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.763 Å
AuthorsJacques, D.A. / Price, A.J. / James, L.C.
Funding support United Kingdom, Australia, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)UK; U10518101 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4453
Polymers32,4092
Non-polymers351
Water6,089338
1
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)16,2051
Polymers16,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2402
Polymers16,2051
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.720, 23.850, 129.549
Angle α, β, γ (deg.)90.000, 96.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 146 / Label seq-ID: 1 - 146

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Capsid protein


Mass: 16204.573 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 133-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: D2ECE2, UniProt: A9PKC6*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: PEG3350 (20%), Ammonium chloride (0.2M, pH 6.3)

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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: Sep 17, 2012
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.763→128.765 Å / Num. all: 25066 / Num. obs: 25066 / % possible obs: 91.9 % / Redundancy: 4.6 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.074 / Rsym value: 0.065 / Net I/av σ(I): 6.509 / Net I/σ(I): 13.3 / Num. measured all: 115457
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.763-1.864.60.2273.21450631880.1150.227580.6
1.86-1.974.70.1534.71501831980.0770.153786.3
1.97-2.14.60.116.21432831110.0560.119.789.9
2.1-2.274.40.08971327129860.0450.08912.191.1
2.27-2.494.40.0827.31252528710.0430.08213.695.3
2.49-2.784.50.0748.11206426730.0390.07416.197.7
2.78-3.214.80.0610.41147623930.0310.0619.298.7
3.21-3.944.90.0589.91009620750.0290.05821.999.1
3.94-5.574.90.05111.4793116250.0260.05122.499.5
5.57-39.8684.50.0517.742429460.0270.05118.999.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.76 Å39.87 Å
Translation1.76 Å39.87 Å

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SCALA3.3.20data scaling
PHASER2.5.7phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4E

3h4e


Resolution: 1.763→128.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2463 / WRfactor Rwork: 0.2074 / FOM work R set: 0.8555 / SU B: 2.7 / SU ML: 0.088 / SU R Cruickshank DPI: 0.155 / SU Rfree: 0.1368 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / 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
Rfree0.2241 1229 4.9 %RANDOM
Rwork0.1899 ---
obs0.1916 23827 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 90.96 Å2 / Biso mean: 28.533 Å2 / Biso min: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å21 Å2
2---0.79 Å20 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 1.763→128.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 1 338 2572
Biso mean--24.73 38.52 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192346
X-RAY DIFFRACTIONr_bond_other_d0.0040.022225
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9433210
X-RAY DIFFRACTIONr_angle_other_deg1.12235126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1345303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39125.25897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56415379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.351510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212696
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02510
X-RAY DIFFRACTIONr_mcbond_it2.5243.4141200
X-RAY DIFFRACTIONr_mcbond_other2.5063.4111199
X-RAY DIFFRACTIONr_mcangle_it3.4545.7381507
Refine LS restraints NCS

Ens-ID: 1 / Number: 15594 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.763→1.808 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 64 -
Rwork0.233 1522 -
all-1586 -
obs--80.26 %

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