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- PDB-7rar: Structure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer -

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Basic information

Entry
Database: PDB / ID: 7rar
TitleStructure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
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
IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBester, S.M. / Kvaratskhelia, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI157802 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32-AI150547 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54-AI150472 United States
CitationJournal: Mbio / Year: 2022
Title: Structural and Mechanistic Bases of Viral Resistance to HIV-1 Capsid Inhibitor Lenacapavir.
Authors: Bester, S.M. / Adu-Ampratwum, D. / Annamalai, A.S. / Wei, G. / Briganti, L. / Murphy, B.C. / Haney, R. / Fuchs, J.R. / Kvaratskhelia, M.
History
DepositionJul 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,37511
Polymers25,4711
Non-polymers90310
Water3,171176
1
C: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)158,24766
Polymers152,8286
Non-polymers5,41960
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 area24920 Å2
ΔGint-404 kcal/mol
Surface area56930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.849, 91.849, 57.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z

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Components

#1: Protein Capsid protein p24 / / CA


Mass: 25471.291 Da / Num. of mol.: 1 / Mutation: A14C, E45C, Q67H, W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.425M NaI, 4% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.15→46.75 Å / Num. obs: 15259 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 27.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.182 / Net I/σ(I): 12.2
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1325 / CC1/2: 0.667 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 2.15→46.75 Å / SU ML: 0.2285 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 734 4.81 %
Rwork0.208 14513 -
obs0.2096 15247 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.65 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 10 176 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451688
X-RAY DIFFRACTIONf_angle_d0.7172297
X-RAY DIFFRACTIONf_chiral_restr0.0481258
X-RAY DIFFRACTIONf_plane_restr0.0057300
X-RAY DIFFRACTIONf_dihedral_angle_d16.3874640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.320.29951300.26212891X-RAY DIFFRACTION99.7
2.32-2.550.25841320.23552901X-RAY DIFFRACTION100
2.55-2.920.26221360.22232884X-RAY DIFFRACTION100
2.92-3.680.24121750.19542889X-RAY DIFFRACTION100
3.68-46.750.21491610.18932948X-RAY DIFFRACTION99.9
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)
12.60758129061-0.274589865893-0.387987940892.10189088686-0.4708493565692.593775820570.008401705395770.258120178657-0.0157308331963-0.228798769633-0.106781354557-0.05855200224070.1262021223990.09520528645590.07996544019370.138133028227-0.0184006174486-0.003562699849180.1554578054350.007243717219670.15921215587123.9599601231-8.22480866255-24.9112026517
24.389542824952.28820482474-0.5520406189055.82324154273-2.305626612153.37256336843-0.0689065799448-0.0956429004332-0.04356531825630.00750109926706-0.0705705067794-0.06387113191820.125350779538-0.002289407550930.1261901104190.2320435259630.05584347749930.03119344558550.207922132628-0.0111207721730.20498584621116.5178015288-31.5334991689-0.741920485096
34.105700831680.6567487762523.743281468893.41268488959-2.200589606939.367480206890.254352558461-0.399016258083-0.6140530830690.0224473532767-0.02302156346930.197038184480.771876883083-0.220123704977-0.2047911225870.317662409422-0.05258884100170.04002291112120.1701378938240.02474301913990.3867857110618.49261723696-43.2306798142-2.26028743188
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: C / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'C' and (resid 1 through 144 )1 - 1441 - 146
22chain 'C' and (resid 145 through 195 )145 - 195147 - 188
33chain 'C' and (resid 196 through 219 )196 - 219189 - 212

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