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- PDB-3gv2: X-ray Structure of Hexameric HIV-1 CA -

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Basic information

Entry
Database: PDB / ID: 3gv2
TitleX-ray Structure of Hexameric HIV-1 CA
ComponentsCapsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
KeywordsVIRAL PROTEIN / Hexameric retroviral capsid
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / viral budding via host ESCRT complex / photosynthesis / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane ...structural constituent of carboxysome shell / carboxysome / carbon fixation / viral budding via host ESCRT complex / photosynthesis / 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
Carboxysome shell protein CcmK / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Gag protein p6 ...Carboxysome shell protein CcmK / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / 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.
Similarity search - Domain/homology
Gag polyprotein / Carboxysome shell protein CcmK4
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Synechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 7 Å
AuthorsKelly, B.N.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: X-ray structures of the hexameric building block of the HIV capsid.
Authors: Pornillos, O. / Ganser-Pornillos, B.K. / Kelly, B.N. / Hua, Y. / Whitby, F.G. / Stout, C.D. / Sundquist, W.I. / Hill, C.P. / Yeager, M.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_mutation ..._entity.pdbx_description / _entity.pdbx_mutation / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.pdbx_descriptor / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.5Nov 1, 2017Group: Refinement description / Category: software
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
B: Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
C: Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
D: Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
E: Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
F: Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4


Theoretical massNumber of molelcules
Total (without water)223,8646
Polymers223,8646
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.618, 156.437, 196.644
Angle α, β, γ (deg.)90.000, 100.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4 / Pr55Gag


Mass: 37310.672 Da / Num. of mol.: 6
Fragment: UNP residues 133-351 of Capsid protein p24, UNP residues 1-109 of CCMK
Mutation: W184A,M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5), (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: isolate NY5, PCC 6803 / Kazusa / Description: FUSION GENE / Gene: gag, ccmK4, slr1839 / Plasmid: Pet11A modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21codon+ / References: UniProt: P12493, UniProt: P73407

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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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole, pH 6.5, 600 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2009
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 15.42 / Number: 30849 / Rmerge(I) obs: 0.114 / Χ2: 0.89 / D res high: 7 Å / D res low: 50 Å / Num. obs: 4325 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
14.965010010.0460.8657.3
11.9314.9610010.0730.8327.6
10.4311.9399.510.0740.9177.2
9.4910.4310010.0831.0017.3
8.819.4910010.1240.9527.3
8.298.8110010.1430.9237.1
7.888.2910010.1990.9357.1
7.547.8899.310.3010.7747
7.257.5498.910.2920.8376.9
77.2598.510.3230.816.5
ReflectionResolution: 7→50 Å / Num. all: 4342 / Num. obs: 4325 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.114 / Χ2: 0.887 / Net I/σ(I): 15.417
Reflection shellResolution: 7→7.25 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.323 / Num. unique all: 402 / Χ2: 0.81 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7→49.754 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.724 / SU ML: 8.9 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ML / Details: THE COORDINATES CONTAIN ONLY BACKBONE ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.323 407 10 %thin shell r-free selection with 6d_dataman
Rwork0.282 ---
obs0.286 4070 92.67 %-
all-4342 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 100 Å2 / Biso mean: 43.249 Å2 / Biso min: 16.55 Å2
Baniso -1Baniso -2Baniso -3
1-139.209 Å20 Å2-3.203 Å2
2--161.115 Å2-0 Å2
3---220.835 Å2
Refinement stepCycle: LAST / Resolution: 7→49.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5256 0 0 0 5256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01910446
X-RAY DIFFRACTIONf_angle_d2.48314196
X-RAY DIFFRACTIONf_chiral_restr0.151596
X-RAY DIFFRACTIONf_plane_restr0.0161866
X-RAY DIFFRACTIONf_dihedral_angle_d21.2833948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
7-7.9540.3591280.31211051233123386
7.954-10.0080.2781370.25412641401140195
10.008-49.7560.3331420.29112941436143697

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