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- PDB-6h09: HIV capsid hexamer with IP6 ligand -

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Basic information

Entry
Database: PDB / ID: 6h09
TitleHIV capsid hexamer with IP6 ligand
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / HIV
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / 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) ...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) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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
INOSITOL HEXAKISPHOSPHATE / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsJames, L.C.
CitationJournal: Elife / Year: 2018
Title: IP6 is an HIV pocket factor that prevents capsid collapse and promotes DNA synthesis.
Authors: Mallery, D.L. / Marquez, C.L. / McEwan, W.A. / Dickson, C.F. / Jacques, D.A. / Anandapadamanaban, M. / Bichel, K. / Towers, G.J. / Saiardi, A. / Bocking, T. / James, L.C.
History
DepositionJul 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2Oct 7, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_conn
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_dist_value ..._chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1642
Polymers24,5041
Non-polymers6601
Water3,081171
1
A: Gag polyprotein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)150,98512
Polymers147,0256
Non-polymers3,9606
Water1086
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 area18500 Å2
ΔGint-222 kcal/mol
Surface area58760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.099, 91.099, 57.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-501-

IHP

21A-501-

IHP

31A-501-

IHP

41A-765-

HOH

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Components

#1: Protein Gag polyprotein / Pr55Gag


Mass: 24504.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: P12493
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: batch mode / Details: PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.987 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Mar 3, 2017
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→78.9 Å / Num. obs: 18396 / % possible obs: 99.7 % / Redundancy: 4.9 % / Net I/σ(I): 2
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.4 / Rrim(I) all: 0.898 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing
RefinementResolution: 2→46.3 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.884 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 928 5.2 %RANDOM
Rwork0.2377 ---
obs0.23914 16819 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.259 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å2-0 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 36 171 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0141664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171501
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.6652269
X-RAY DIFFRACTIONr_angle_other_deg0.9851.6223535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.8915.639227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47922.46877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97215280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9951512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022124
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02276
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_it2.2192.61838
X-RAY DIFFRACTIONr_mcbond_other2.2192.607837
X-RAY DIFFRACTIONr_mcangle_it3.3173.8871049
X-RAY DIFFRACTIONr_mcangle_other3.3153.891050
X-RAY DIFFRACTIONr_scbond_it2.9892.907826
X-RAY DIFFRACTIONr_scbond_other2.9932.899824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6854.2321217
X-RAY DIFFRACTIONr_long_range_B_refined5.84430.2891838
X-RAY DIFFRACTIONr_long_range_B_other5.84230.321839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 66 -
Rwork0.335 1247 -
obs--97.33 %

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