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- PDB-6v2f: Crystal structure of the HIV capsid hexamer bound to the small mo... -

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Basic information

Entry
Database: PDB / ID: 6v2f
TitleCrystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, GS-6207
ComponentsHIV-1 capsid
KeywordsVIRAL PROTEIN / HIV capsid / capsid assembly accelerator / long-acting inhibitor / antiviral
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / cytoplasm
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
Chem-QNG / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAppleby, T.C. / Link, J.O. / Yant, S.R. / Villasenor, A.G. / Somoza, J.R. / Hu, E.Y. / Schroeder, S.D. / Cihlar, T.
CitationJournal: Nature / Year: 2020
Title: Clinical targeting of HIV capsid protein with a long-acting small molecule.
Authors: Link, J.O. / Rhee, M.S. / Tse, W.C. / Zheng, J. / Somoza, J.R. / Rowe, W. / Begley, R. / Chiu, A. / Mulato, A. / Hansen, D. / Singer, E. / Tsai, L.K. / Bam, R.A. / Chou, C.H. / Canales, E. / ...Authors: Link, J.O. / Rhee, M.S. / Tse, W.C. / Zheng, J. / Somoza, J.R. / Rowe, W. / Begley, R. / Chiu, A. / Mulato, A. / Hansen, D. / Singer, E. / Tsai, L.K. / Bam, R.A. / Chou, C.H. / Canales, E. / Brizgys, G. / Zhang, J.R. / Li, J. / Graupe, M. / Morganelli, P. / Liu, Q. / Wu, Q. / Halcomb, R.L. / Saito, R.D. / Schroeder, S.D. / Lazerwith, S.E. / Bondy, S. / Jin, D. / Hung, M. / Novikov, N. / Liu, X. / Villasenor, A.G. / Cannizzaro, C.E. / Hu, E.Y. / Anderson, R.L. / Appleby, T.C. / Lu, B. / Mwangi, J. / Liclican, A. / Niedziela-Majka, A. / Papalia, G.A. / Wong, M.H. / Leavitt, S.A. / Xu, Y. / Koditek, D. / Stepan, G.J. / Yu, H. / Pagratis, N. / Clancy, S. / Ahmadyar, S. / Cai, T.Z. / Sellers, S. / Wolckenhauer, S.A. / Ling, J. / Callebaut, C. / Margot, N. / Ram, R.R. / Liu, Y.P. / Hyland, R. / Sinclair, G.I. / Ruane, P.J. / Crofoot, G.E. / McDonald, C.K. / Brainard, D.M. / Lad, L. / Swaminathan, S. / Sundquist, W.I. / Sakowicz, R. / Chester, A.E. / Lee, W.E. / Daar, E.S. / Yant, S.R. / Cihlar, T.
History
DepositionNov 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 2, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 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
A: HIV-1 capsid
B: HIV-1 capsid
C: HIV-1 capsid
D: HIV-1 capsid
E: HIV-1 capsid
F: HIV-1 capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,36512
Polymers153,5556
Non-polymers5,8106
Water15,331851
1
A: HIV-1 capsid
hetero molecules

A: HIV-1 capsid
hetero molecules

A: HIV-1 capsid
hetero molecules

B: HIV-1 capsid
hetero molecules

B: HIV-1 capsid
hetero molecules

B: HIV-1 capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,36512
Polymers153,5556
Non-polymers5,8106
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 operation1_554x,y,z-11
crystal symmetry operation2_554-y,x-y,z-11
crystal symmetry operation3_554-x+y,-x,z-11
Buried area14500 Å2
ΔGint-104 kcal/mol
Surface area56590 Å2
MethodPISA
2
C: HIV-1 capsid
hetero molecules

C: HIV-1 capsid
hetero molecules

C: HIV-1 capsid
hetero molecules

D: HIV-1 capsid
hetero molecules

D: HIV-1 capsid
hetero molecules

D: HIV-1 capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,36512
Polymers153,5556
Non-polymers5,8106
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_664-y+1,x-y+1,z-11
crystal symmetry operation3_564-x+y,-x+1,z-11
Buried area14860 Å2
ΔGint-100 kcal/mol
Surface area56880 Å2
MethodPISA
3
E: HIV-1 capsid
F: HIV-1 capsid
hetero molecules

E: HIV-1 capsid
F: HIV-1 capsid
hetero molecules

E: HIV-1 capsid
F: HIV-1 capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,36512
Polymers153,5556
Non-polymers5,8106
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14740 Å2
ΔGint-108 kcal/mol
Surface area56080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.301, 158.301, 55.648
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z

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Components

#1: Protein
HIV-1 capsid


Mass: 25592.469 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#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.: 6 / Source method: obtained synthetically / Formula: C39H32ClF10N7O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiretroviral*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 12% PEG 3350, 0.2 M sodium thiocyanate, 0.1 M sodium cacodylate, pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→29.92 Å / Num. obs: 105922 / % possible obs: 98.66 % / Redundancy: 5.2 % / Biso Wilson estimate: 29.52 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.058 / Rrim(I) all: 0.132 / Net I/σ(I): 18.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 10274 / CC1/2: 0.758 / Rpim(I) all: 0.427 / Rrim(I) all: 0.905 / % possible all: 90.82

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47

3h47


Resolution: 2→29.92 Å / SU ML: 0.2338 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.0908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2508 1968 1.88 %
Rwork0.2087 102700 -
obs0.2095 104668 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 2→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9447 0 384 851 10682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003710062
X-RAY DIFFRACTIONf_angle_d0.636813767
X-RAY DIFFRACTIONf_chiral_restr0.04041503
X-RAY DIFFRACTIONf_plane_restr0.00441719
X-RAY DIFFRACTIONf_dihedral_angle_d17.61593725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.2641350.25777151X-RAY DIFFRACTION97.21
2.05-2.110.2751460.23537297X-RAY DIFFRACTION99.23
2.11-2.170.27591420.22467346X-RAY DIFFRACTION98.86
2.17-2.240.31721400.21637331X-RAY DIFFRACTION99.11
2.24-2.320.25761400.20437251X-RAY DIFFRACTION99.14
2.32-2.410.24151440.21037376X-RAY DIFFRACTION99.66
2.41-2.520.27881430.20987337X-RAY DIFFRACTION99.23
2.52-2.650.25291460.21277392X-RAY DIFFRACTION99.62
2.65-2.820.26541320.20897307X-RAY DIFFRACTION99.65
2.82-3.040.26691420.22117384X-RAY DIFFRACTION99.87
3.04-3.340.25451400.21567388X-RAY DIFFRACTION99.91
3.34-3.820.24561340.19997381X-RAY DIFFRACTION100
3.82-4.810.21651430.18537379X-RAY DIFFRACTION99.92
4.82-29.920.24421410.21217380X-RAY DIFFRACTION99.67

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