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- PDB-7rhm: Structure of Q67H/N74D mutant of disulfide stabilized HIV-1 CA hexamer -

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Basic information

Entry
Database: PDB / ID: 7rhm
TitleStructure of Q67H/N74D mutant of disulfide stabilized HIV-1 CA hexamer
ComponentsCAPSID PROTEIN P24
KeywordsViral Protein/Inhibitor / inhibitor / viral protein / Viral Protein-Inhibitor complex
Function / homology
Function and homology information


viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
: / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...: / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / 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: 2.16 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)R01AI062520 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143649 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 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)26,15710
Polymers25,4721
Non-polymers6859
Water3,117173
1
C: CAPSID PROTEIN P24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,94360
Polymers152,8346
Non-polymers4,10954
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 area24010 Å2
ΔGint-437 kcal/mol
Surface area58720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.116, 92.116, 57.837
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
Components on special symmetry positions
IDModelComponents
11C-573-

HOH

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Components

#1: Protein CAPSID PROTEIN P24


Mass: 25472.275 Da / Num. of mol.: 1 / Mutation: A14C, E45C, Q67H, N74D, W184A, M185A,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.35M NaI, 3% 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 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.16→46.83 Å / Num. obs: 15160 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 24.85 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.8
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1303 / CC1/2: 0.608 / % 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: 2.16→46.83 Å / SU ML: 0.2847 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 726 4.79 %
Rwork0.2313 14417 -
obs0.2327 15143 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.81 Å2
Refinement stepCycle: LAST / Resolution: 2.16→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 9 173 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151725
X-RAY DIFFRACTIONf_angle_d0.41772350
X-RAY DIFFRACTIONf_chiral_restr0.0371266
X-RAY DIFFRACTIONf_plane_restr0.0042308
X-RAY DIFFRACTIONf_dihedral_angle_d16.719645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.330.35181250.31052874X-RAY DIFFRACTION99.67
2.33-2.560.29191330.26322870X-RAY DIFFRACTION99.83
2.56-2.930.23191320.25112891X-RAY DIFFRACTION99.97
2.93-3.690.24591750.21312851X-RAY DIFFRACTION100
3.69-46.830.25051610.20272931X-RAY DIFFRACTION99.97
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)
11.137504213090.419213582134-0.4594290116011.46159773579-0.942918884111.71822448179-0.01471437130640.1294764240440.0620396916352-0.160413924337-0.07869932205710.01378875871420.08863650525910.06773875360830.09789695740260.1496185455420.00278362129105-0.01593532370630.14699841382-0.006858197643060.16077858474623.5001863278-10.1652925576-21.7863373161
22.217262321470.9681636721521.76919490317.29933093082-0.841157914872.47833137849-0.0702938776039-0.00484431048841-0.315413504805-0.534831753635-0.0325558647789-0.2910097760050.42053115310.1749724111260.1127207199680.2136827919460.03559824550660.06254633469410.171423097763-0.001970744272830.2515129891613.61119262-36.8669792195-3.63066587261
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 160 )1 - 1601 - 161
22chain 'C' and (resid 161 through 220 )161 - 219162 - 220

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