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- PDB-6r6q: HIV capsid hexamer with IP5 ligand -

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Basic information

Entry
Database: PDB / ID: 6r6q
TitleHIV capsid hexamer with IP5 ligand
ComponentsGag polyproteinGroup-specific antigen
KeywordsVIRAL PROTEIN / HIV
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
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 ...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 / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsJames, L.C.
CitationJournal: to be published
Title: HIV hexamer
Authors: James, L.C.
History
DepositionMar 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)24,5041
Polymers24,5041
Non-polymers00
Water0
1
A: Gag polyprotein
x 6


Theoretical massNumber of molelcules
Total (without water)147,0256
Polymers147,0256
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area14250 Å2
ΔGint-108 kcal/mol
Surface area59070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.693, 90.693, 56.958
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Gag polyprotein / Group-specific antigen


Mass: 24504.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0, UniProt: P12493*PLUS

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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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 293 K / Method: batch mode / Details: PEG 6K, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 Å
DetectorType: OXFORD SAPPHIRE CCD / Detector: CCD / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.73→78 Å / Num. obs: 7234 / % possible obs: 92.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5
Reflection shellResolution: 2.73→2.79 Å / Rmerge(I) obs: 0.582 / Num. unique obs: 956 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Adxvdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ES8

6es8


Resolution: 2.73→78 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / SU B: 15.752 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28881 362 4.5 %RANDOM
Rwork0.22086 ---
obs0.22401 6874 92.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.117 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.44 Å20 Å2
2--0.87 Å2-0 Å2
3----2.82 Å2
Refinement stepCycle: 1 / Resolution: 2.73→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 0 0 1580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131716
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171556
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6732358
X-RAY DIFFRACTIONr_angle_other_deg1.241.5683629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.8065.43221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38322.93375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35515281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9521511
X-RAY DIFFRACTIONr_chiral_restr0.0620.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022100
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02317
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7814.214833
X-RAY DIFFRACTIONr_mcbond_other2.7694.213832
X-RAY DIFFRACTIONr_mcangle_it4.4276.3031041
X-RAY DIFFRACTIONr_mcangle_other4.4276.3051042
X-RAY DIFFRACTIONr_scbond_it2.9274.874882
X-RAY DIFFRACTIONr_scbond_other2.934.862879
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6337.2921312
X-RAY DIFFRACTIONr_long_range_B_refined7.07549.4051840
X-RAY DIFFRACTIONr_long_range_B_other7.08249.4361841
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.73→2.801 Å
RfactorNum. reflection% reflection
Rfree0.45 13 -
Rwork0.247 523 -
obs--99.81 %

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