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- PDB-7rj2: Co-crystal structure of lenacapavir bound to Q67H/N74D mutant of ... -

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Basic information

Entry
Database: PDB / ID: 7rj2
TitleCo-crystal structure of lenacapavir bound to 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 / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / 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 ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Chem-QNG / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 20, 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 / Structure summary / Category: chem_comp / citation / Item: _chem_comp.pdbx_synonyms / _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.5Dec 25, 2024Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7097
Polymers25,4721
Non-polymers1,2376
Water3,405189
1
C: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)160,25642
Polymers152,8346
Non-polymers7,42236
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 area21360 Å2
ΔGint-398 kcal/mol
Surface area57200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.183, 92.183, 57.965
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-531-

HOH

21C-587-

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-QNG / Lenacapavir / Sunlenca / GS-CA1 / GS-6207


Mass: 968.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H32ClF10N7O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.425M NaI, 6% 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 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.32→46.91 Å / Num. obs: 12256 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 28.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.5
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3 / Num. unique obs: 2373 / CC1/2: 0.835 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VKV

6vkv


Resolution: 2.32→39.92 Å / SU ML: 0.2266 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 604 4.93 %
Rwork0.1987 11649 -
obs0.2011 12253 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.58 Å2
Refinement stepCycle: LAST / Resolution: 2.32→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 69 189 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611827
X-RAY DIFFRACTIONf_angle_d0.92442521
X-RAY DIFFRACTIONf_chiral_restr0.0466263
X-RAY DIFFRACTIONf_plane_restr0.0056309
X-RAY DIFFRACTIONf_dihedral_angle_d16.205672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.550.26761280.23292891X-RAY DIFFRACTION99.93
2.55-2.920.26431400.19452904X-RAY DIFFRACTION100
2.92-3.680.26371730.20412893X-RAY DIFFRACTION99.64
3.68-39.920.22291630.18682961X-RAY DIFFRACTION99.62
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)
12.727944956380.140908550402-0.1237394929311.980989550350.537800393453.261712106890.0290598520432-0.278363201624-0.03573512404260.256057489941-0.138084294554-0.02477838250950.146230982509-0.1136421622140.09852918343320.1612673940440.00798144387679-0.002630548918610.120794223864-0.01388851197980.184306207426-24.0028646816-8.0081111159933.1898434894
24.33359088527-1.382578918670.6541410280546.288662952752.569833544052.61608020662-0.05330470775480.195134022792-0.01076579873060.116509958548-0.07469423830630.2091951934070.184868489633-0.171373422380.1415450390190.185682002849-0.04526836715920.02877882560030.2068385416940.03730263029310.179730657347-16.4144537416-32.23449573419.0304864925
35.526886235280.2947922887923.843996722625.976881877283.683603380965.016501190250.2931915446140.245081678036-0.3015601158110.272192393875-0.188782741569-0.4659652814011.076965270540.0130842007115-0.1560173148230.3219837909540.02120740915050.06478246981450.218960936126-0.04137370427460.332146586634-8.47781492545-43.351425870710.7909090919
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 145 )1 - 1451 - 145
22chain 'C' and (resid 146 through 195 )146 - 195146 - 187
33chain 'C' and (resid 196 through 219 )196 - 219188 - 211

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