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- PDB-7rhn: Co-crystal structure of Q67H mutant of disulfide stabilized HIV-1... -

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Basic information

Entry
Database: PDB / ID: 7rhn
TitleCo-crystal structure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer and lenacapavir
ComponentsCapsid protein p24
KeywordsViral Protein/Inhibitor / inhibitor / viral protein / Viral Protein-Inhibitor complex
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 / Chem-QNG / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 / 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

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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)26,9629
Polymers25,4711
Non-polymers1,4918
Water84747
1
C: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,77354
Polymers152,8286
Non-polymers8,94548
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 area24070 Å2
ΔGint-399 kcal/mol
Surface area56900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.730, 89.730, 56.092
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-414-

HOH

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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-QNG / N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide / Lenacapavir / Lenacapavir


Mass: 968.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H32ClF10N7O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


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


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


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.35M 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: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.46→45.48 Å / Num. obs: 9492 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 35.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Net I/σ(I): 12.6
Reflection shellResolution: 2.46→2.56 Å / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1063 / CC1/2: 0.751

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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: 2.46→45.48 Å / SU ML: 0.3404 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9382
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2884 458 4.83 %
Rwork0.2417 9025 -
obs0.2439 9483 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.38 Å2
Refinement stepCycle: LAST / Resolution: 2.46→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 71 47 1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271797
X-RAY DIFFRACTIONf_angle_d0.68972480
X-RAY DIFFRACTIONf_chiral_restr0.0412261
X-RAY DIFFRACTIONf_plane_restr0.0052301
X-RAY DIFFRACTIONf_dihedral_angle_d18.086656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.820.32081460.30042984X-RAY DIFFRACTION99.81
2.82-3.550.28831590.25152986X-RAY DIFFRACTION99.97
3.55-45.480.27881530.21843055X-RAY DIFFRACTION100
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)
11.78337871682-0.8904119373391.195434528861.92590278462-2.116256472292.3958933277-0.3049972113460.0254199794355-0.690614754823-0.949425677137-0.3324512056280.63420044574-0.946847130915-1.368656322780.4767754650260.582200131991-0.00607933992832-0.1249921177290.604023735066-0.1689308113590.4708296673111.3721407345-3.16902560524-34.233618453
21.067703026240.800845232096-0.09072987315352.76673307207-0.9865021273452.69315772446-0.0365682336732-0.127360396285-0.1039366659550.17824277298-0.172764454657-0.04238913902490.135432195719-0.1722008284870.1933362599880.2048721147530.003394483894510.008335176714580.283294796402-0.005943606542850.26183162427614.8673997015-8.93618364326-15.0125592514
31.92963669721-0.390974889591-0.5236254222771.516961292560.1067025457052.788531359080.07824872271460.09201678240550.232928138385-0.141768653453-0.0300958794366-0.351789236057-0.0747135512090.0615952016214-0.0435313205810.227471242208-0.00361354132048-0.02946951112950.3099010733760.008032680498060.30934032892929.7931151706-8.4220848056-18.7179990813
40.4425913578280.4499424801360.205205800752.11679170967-1.34317589483.279768740050.2275769833130.5674677548210.366073737164-0.35927396723-0.260427915099-0.0773785043618-0.07956790244531.419861853850.0121033396790.3770849413320.05796862627780.0469669148340.6987537867880.0605875518560.3177560019434.0385784066-4.67456821846-35.7789246389
53.23501329986-0.2896113104941.918622392475.09984668402-0.03120482871897.649011650470.3067206160131.569088276810.177630736273-0.8631682746410.1526538287090.009493322288790.5037706515550.249529634267-0.3610432868050.4666507207310.01694449113580.009441348024080.432853308730.03144101385840.34122710992324.189049908-6.03885153581-37.4514140487
63.376385273240.741447867762-1.839584034115.25341803801-3.808820445993.99736816936-0.425251311509-0.223798061308-0.000981785918624-0.745526620858-0.623794020804-0.03411713392830.8691468106480.8490490899430.8213996021230.3633897996960.01197082754890.05492188241810.2725388156360.04659674386320.30542560633525.9229083984-15.1579061592-19.2881340736
72.805642925060.9353877297350.1768833304462.70305901205-0.9071867239191.72746820304-0.206047835125-0.0610666370440.3201709748830.3275476118570.261800519970.117944730406-0.0828151016677-0.1593465621790.08392968974870.373948126997-0.0191402645386-0.02721974091540.3780015840890.01049923118390.22682347914417.7000518493-28.70301401633.39597784822
88.859054880730.8421884573550.3680993034536.12695335994-2.046215137747.24835468016-0.314856777689-0.6645680905740.8647850745050.2765849457820.260220132476-0.02676775965340.0932796798204-0.67572510087-0.0002122033696950.2707628002230.06202951472690.00513114185950.275504137509-0.02596231417740.26730734078613.7570659167-28.6892090634-2.98838321631
96.295203739945.08413688797-3.112220019595.11995567084-4.188208658935.38936423739-0.2664635601370.094873044885-1.15688359097-0.2457953887040.00691980034636-0.8064902785241.11672408760.7564048073610.3455755413850.3161702590940.0742845684939-0.005383709080420.338110341103-0.07045445086730.43582910976117.4171512873-37.1309863877-2.20078533872
103.371816115871.3154466243.038809685933.377212802890.5079402525383.3201286006-0.0389661830462-0.391850754636-0.326996950105-0.313577109974-0.470118501112-0.2525684047220.859131121905-0.5061210419720.5041680616570.481759868635-0.02087662790630.01492760624760.2857440049020.0441522760950.4346728633767.94116915045-42.4969823133-1.60092201327
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 16 )1 - 161 - 16
22chain 'C' and (resid 17 through 48 )17 - 4817 - 48
33chain 'C' and (resid 49 through 83 )49 - 8349 - 84
44chain 'C' and (resid 84 through 110 )84 - 11085 - 108
55chain 'C' and (resid 111 through 125 )111 - 125109 - 123
66chain 'C' and (resid 126 through 144 )126 - 144124 - 142
77chain 'C' and (resid 145 through 160 )145 - 160143 - 158
88chain 'C' and (resid 161 through 175 )161 - 175159 - 173
99chain 'C' and (resid 176 through 195 )176 - 195174 - 184
1010chain 'C' and (resid 196 through 219 )196 - 219185 - 208

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