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- PDB-6bhr: HIV-1 immature CTD-SP1 hexamer in complex with IP6 -

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Basic information

Entry
Database: PDB / ID: 6bhr
TitleHIV-1 immature CTD-SP1 hexamer in complex with IP6
ComponentsCapsid protein p24,Spacer peptide 1
KeywordsVIRAL PROTEIN / assembly / co-factor
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Retrovirus capsid C-terminal domain / 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 domain / 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
INOSITOL HEXAKISPHOSPHATE / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.908 Å
AuthorsZadrozny, K. / Wagner, J.M. / Ganser-Pornillos, B.K. / Pornillos, O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI129678 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM103297 United States
CitationJournal: Nature / Year: 2018
Title: Inositol phosphates are assembly co-factors for HIV-1.
Authors: Dick, R.A. / Zadrozny, K.K. / Xu, C. / Schur, F.K.M. / Lyddon, T.D. / Ricana, C.L. / Wagner, J.M. / Perilla, J.R. / Ganser-Pornillos, B.K. / Johnson, M.C. / Pornillos, O. / Vogt, V.M.
History
DepositionOct 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.6Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Capsid protein p24,Spacer peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1372
Polymers10,4771
Non-polymers6601
Water181
1
G: Capsid protein p24,Spacer peptide 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)66,82212
Polymers62,8626
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 area14450 Å2
ΔGint-167 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.939, 70.939, 42.041
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
11G-401-

IHP

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Components

#1: Protein Capsid protein p24,Spacer peptide 1 /


Mass: 10476.955 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 (isolate BH10)
Production host: Escherichia coli (E. coli) / References: UniProt: P03347
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


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


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion / Details: 0.2 M NaCl 20% PEG 3350 0.1 M Bis-Tris pH 5.35

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 2665 / % possible obs: 96.3 % / Redundancy: 8.1 % / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I4T

5i4t


Resolution: 2.908→35.469 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 129 6.1 %
Rwork0.2154 --
obs0.2188 2115 76.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.908→35.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms668 0 36 1 705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005715
X-RAY DIFFRACTIONf_angle_d1.09982
X-RAY DIFFRACTIONf_dihedral_angle_d11.106434
X-RAY DIFFRACTIONf_chiral_restr0.831113
X-RAY DIFFRACTIONf_plane_restr0.004121
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)
10.0463-0.03760.01550.07640.00670.1656-0.1553-0.0184-0.0878-0.17290.0315-0.05730.0865-0.0389-0.1345-0.0113-0.28410.0189-0.06970.07890.3524-12.7976-15.9015-3.0848
20.0119-0.0051-0.00950.0079-0.00470.0162-0.0928-0.0528-0.1084-0.1793-0.05110.10750.178-0.0309-0.26490.2563-0.1377-0.0003-0.13140.3555-0.0455-17.9965-22.23261.5152
30.03190.0283-0.00280.0380.01510.0085-0.0210.0402-0.0307-0.12990.13270.1076-0.0958-0.0510.0060.3190.1180.06810.33280.11980.1479-22.056-11.85317.1936
40.0225-0.01430.05440.0751-0.12720.2512-0.0224-0.05180.04080.0508-0.05120.02170.04320.0041-0.11050.30380.02330.06760.36410.07510.157-7.9327-6.193120.905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 280 through 306 )
2X-RAY DIFFRACTION2chain 'G' and (resid 307 through 337 )
3X-RAY DIFFRACTION3chain 'G' and (resid 338 through 354 )
4X-RAY DIFFRACTION4chain 'G' and (resid 355 through 370 )

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