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- PDB-7rj4: Co-crystal structure of lenacapavir bound to N74D mutant of disul... -

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Basic information

Entry
Database: PDB / ID: 7rj4
TitleCo-crystal structure of lenacapavir bound to 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 process / viral nucleocapsid / host cell cytoplasm / 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) / 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 knuckle ...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 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: 3.32 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 1.1Aug 17, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.2Oct 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 1.3Nov 9, 2022Group: Database references / Structure summary / Category: chem_comp / citation / Item: _chem_comp.pdbx_synonyms / _citation.journal_volume
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: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
C: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,31027
Polymers76,3873
Non-polymers3,92424
Water2,378132
1
A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
hetero molecules

A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
hetero molecules

A: CAPSID PROTEIN P24
B: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,62154
Polymers152,7746
Non-polymers7,84748
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2
C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules

C: CAPSID PROTEIN P24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,62154
Polymers152,7746
Non-polymers7,84748
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
Unit cell
Length a, b, c (Å)159.089, 159.089, 56.984
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 5 or (resid 6...
d_2ens_1(chain "B" and (resid 1 through 6 or resid 8...
d_3ens_1(chain "C" and (resid 1 through 5 or (resid 6...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROLEUA1 - 6
d_12ens_1GLYPROA8 - 17
d_13ens_1THRPROA19 - 85
d_14ens_1HISPROA87 - 99
d_15ens_1GLYLEUA101 - 111
d_16ens_1GLULYSA113 - 131
d_17ens_1TRPVALA134 - 143
d_18ens_1METILEA145 - 154
d_19ens_1GLNGLNA156 - 177
d_110ens_1SERGLNA179 - 180
d_111ens_1VALGLUA182 - 188
d_112ens_1LEUVALA190 - 192
d_113ens_1ASNLEUA194 - 212
d_114ens_1GLUGLNA214 - 220
d_21ens_1PROLEUC1 - 6
d_22ens_1GLYPROC8 - 17
d_23ens_1THRPROC19 - 85
d_24ens_1HISPROC87 - 99
d_25ens_1GLYLEUC102 - 112
d_26ens_1GLULYSC114 - 132
d_27ens_1TRPVALC134 - 143
d_28ens_1METILEC146 - 155
d_29ens_1GLNGLNC157 - 180
d_210ens_1VALGLUC182 - 188
d_211ens_1LEUVALC190 - 192
d_212ens_1ASNLEUC194 - 212
d_213ens_1GLUGLNC215 - 221
d_31ens_1PROLEUE1 - 6
d_32ens_1GLYPROE8 - 17
d_33ens_1THRPROE19 - 85
d_34ens_1HISPROE87 - 99
d_35ens_1GLYLEUE101 - 111
d_36ens_1GLULYSE113 - 131
d_37ens_1TRPVALE133 - 142
d_38ens_1METILEE144 - 153
d_39ens_1GLNGLNE155 - 176
d_310ens_1SERGLNE178 - 179
d_311ens_1VALGLUE181 - 187
d_312ens_1LEUVALE189 - 191
d_313ens_1ASNLEUE193 - 211
d_314ens_1GLUGLNE213 - 219

NCS oper:
IDCodeMatrixVector
1given(-0.999721230506, -0.0148677204599, -0.0183415420115), (0.0149831755454, -0.999868687877, -0.00617344741771), (-0.0182473484542, -0.00644654099263, 0.999812720655)158.199950209, -93.2669536361, 1.29946706991
2given(0.0244358888232, -0.999673589373, 0.00745667803601), (-0.999665767728, -0.0244973130131, -0.00826041689733), (0.00844038918535, -0.00725233514463, -0.999938079816)-47.9474193813, 78.3317275137, 25.946785446

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Components

#1: Protein CAPSID PROTEIN P24


Mass: 25462.256 Da / Num. of mol.: 3 / Mutation: A14C, E45C, 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 / 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


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


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.05M 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: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3.32→46.32 Å / Num. obs: 12427 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 82.93 Å2 / CC1/2: 0.963 / Net I/σ(I): 3.1
Reflection shellResolution: 3.32→3.59 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2530 / CC1/2: 0.838

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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: 3.32→46.32 Å / SU ML: 0.5263 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.9198
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3307 586 4.89 %
Rwork0.2778 11402 -
obs0.2804 11988 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.54 Å2
Refinement stepCycle: LAST / Resolution: 3.32→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5047 0 213 132 5392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345413
X-RAY DIFFRACTIONf_angle_d0.70367426
X-RAY DIFFRACTIONf_chiral_restr0.0466808
X-RAY DIFFRACTIONf_plane_restr0.0059947
X-RAY DIFFRACTIONf_dihedral_angle_d16.86242004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.782980625134
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.666611936047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.650.39061250.33812526X-RAY DIFFRACTION86.75
3.65-4.180.34671260.28192930X-RAY DIFFRACTION99.35
4.18-5.270.30561660.26652940X-RAY DIFFRACTION99.97
5.27-46.320.3231690.26253006X-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)
11.34181800998-0.6682798011330.3960518901843.075803394650.2859719242883.05284418885-0.04027809923060.2265993280550.0769872328672-0.4599494140090.0148317226790.004412586639350.2315750333220.16770728947-1.24759077842E-80.718772382657-0.0789081344295-0.07925992173090.5300581245220.06672876363950.6965047506796.4154828189-65.0590009592-6.31083025192
20.9486754224440.232797658375-0.4576252414980.564370903863-0.5066077702622.06658184006-0.858498555583-0.308854702895-0.0300696066757-0.4011019471320.36965186870.4068764593070.351655584531-0.09528544006272.02696718061E-70.6155592944070.00652244441272-0.07821409780720.7042919739530.02829641220090.83623728900874.8240365416-84.121913861615.3896007608
31.40465431563-1.42065093015-0.6083442867191.711590916550.983010156981.146785404520.09673136080.1457201990560.146383114387-0.527025589318-0.193457049261-0.02118444761990.0480878462965-0.395655892591-1.07938930812E-50.539630186260.04294387739440.02632311103030.649099124835-0.02918309167920.68205398832662.6732579694-26.6040524879-6.31112976425
40.519568091630.721657264978-0.3121557012751.774191794940.2204363294480.5446246661740.701630705859-0.872642735501-0.6547294700431.84757357671-0.8596623254940.4800201148740.957500136433-0.2521008102070.03200640611270.730598487865-0.130961799216-0.1767575736610.83793486089-0.07955108559741.2686221600580.2348546295-12.341153222318.4032697799
50.394872114387-0.164366992073-0.5549000389150.4559606419220.7080561567411.245203566740.2771020124340.7405908401410.38574436945-0.4751164469660.04079465675340.167025549744-1.928985605370.6329537888110.00311653161141.11119500618-0.2442094966420.05122186917050.5164281128650.0002163532327920.99657474285388.1051348315-4.8567919957314.359525295
60.7617303980620.590482449876-0.6599712390920.486297634666-0.5256337669020.578804834097-0.50611016205-0.2394450167270.156362530184-0.01682718698670.3010297404340.188301830024-0.324704272592-1.09399709961-0.1983762542190.3441282585850.214165949701-0.2625906920770.568028117841-0.01358881935151.160432546088.24947879082-8.253920108742.8092150164
73.84218997425-0.997919533925-3.069459313580.715906104411.101738554572.828424102790.7386601285341.58953712028-0.2245639688060.037126950264-0.4941397065260.976943601202-1.35962373499-1.943825222070.07505535206330.6122373536190.1022417623490.007644368929930.6518738883170.003970527510460.79954483908215.4690867362-7.9212684858721.5636940733
80.827839514201-0.347989289898-0.4295761394040.2633516814510.6417610406713.077084525920.5459599586290.480767665614-0.2094812398980.64996150279-0.154870086817-0.113727506679-0.263457725271-0.6056549937934.230372863320.496589160996-0.0601035503456-0.2204713028210.832340729475-0.248861049118-1.4855327809914.4707542524-16.127710887628.1768236025
90.0100845347241-0.0534396861123-0.01511103955011.8905810673-1.865339709441.821471450940.341247481853-0.1737385641890.236138104139-0.34375535999-0.653164905851-0.685093120701-0.2401449598460.680836249588-0.9774607316520.6490351374710.01354797263790.7057107631460.5001153674760.145688455876-0.76018295652627.8449445211-23.035807728428.6402775871
100.1521914573830.3852114872620.4062162014322.322661506290.2636269840531.2930241176-0.553877897050.602365985604-0.2168939564621.178547637630.00881319696323-2.297491167481.457171407530.137764315186-0.54028237011.050441216180.129085452591-0.07396251510550.967883842165-0.04236335425940.68527550447923.3061676214-26.378981187247.4931225492
110.589374808256-0.6367669541770.5867073175340.919433887314-0.8410038081050.7332012932910.186846193308-0.682979418002-0.971672304420.5529283532030.4455490096061.300456069641.85811171477-0.2062912857870.1273882819870.816715416098-0.03398064782340.1662425764990.668757213994-0.1186040959280.65899606235216.9625875992-19.527881872143.8016021022
120.9884944724631.08170632489-0.2586284595541.23342780016-0.3123995063020.07607090014950.5766503963640.158208424038-0.489594555021-0.0222785507757-0.505850116437-1.01269543435-0.5917764537990.378960305099-0.2305904142140.616328722892-0.009455317985070.08151864754930.4498273905950.05195372935120.027194470636126.0375643196-14.56803588928.1868288308
130.8819131936560.9505180570510.7951307095490.9693712242830.8782611215270.768168575412-0.2938151415061.39323501871-0.3379144777970.03582141618780.295792725847-0.8348185764480.8804165120420.009679253067730.1885149842850.8273752786830.08659814596930.1575913586330.9055315216540.3012420842290.61713060892735.2867308102-0.8692304905166.46055165872
140.1415132696360.165515479186-0.1073599679230.140998478056-0.06919191892970.05090844404720.4706852226850.057270028614-0.274831992138-0.279878637018-0.9616377802870.872535981930.2275502490420.148224513268-0.001564101945060.4160679399070.0780157581621-0.1566316417280.4529835785870.03232999350180.71630099226832.45954132313.8135481010911.9365097459
150.01308921177980.0147739103440.03470100967640.06745703594730.06037955221580.0673481607770.153929732958-1.92858743692-1.130896421270.316587876824-0.6083580148180.137384211805-0.1215436134340.871422554978-1.56776978911E-61.39491269811-0.4209361334020.09976521917351.23075742024-0.02714294023810.97857505622340.2571704102-1.4527300949320.3451979096
160.04325622830880.03074735190770.2112927821470.02138989909520.05836632490661.60089340511.07855361380.128330009177-0.279810138205-0.0111598750332-0.1082183405930.245645075362-0.3213147869471.573225305590.07773177357110.8613572022250.1099294466350.2904499839990.5945170480470.003766053665391.3430177678544.358032579711.14672408127.26702243999
170.183476684885-0.000635191889534-0.2256986711540.226772410441-0.1060428607810.303248888761-0.2897199466970.09160276536211.40041609462-0.513317388148-0.0120185038808-0.555960362709-0.1064286689310.17008599994-0.001796874736560.502714341527-0.1806203109570.1044137240920.5630539562460.0811238059060.50813588961638.9169406815.964499728813.7789208885
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 144 )AA1 - 1441 - 145
22chain 'A' and (resid 145 through 219 )AA145 - 219146 - 220
33chain 'B' and (resid 1 through 144 )BC1 - 1441 - 146
44chain 'B' and (resid 145 through 174 )BC145 - 174147 - 176
55chain 'B' and (resid 175 through 220 )BC175 - 220177 - 222
66chain 'C' and (resid 1 through 16 )CE1 - 161 - 16
77chain 'C' and (resid 17 through 43 )CE17 - 4317 - 43
88chain 'C' and (resid 44 through 62 )CE44 - 6244 - 62
99chain 'C' and (resid 63 through 83 )CE63 - 8363 - 83
1010chain 'C' and (resid 84 through 104 )CE84 - 10484 - 104
1111chain 'C' and (resid 105 through 125 )CE105 - 125105 - 125
1212chain 'C' and (resid 126 through 144 )CE126 - 144126 - 144
1313chain 'C' and (resid 145 through 160 )CE145 - 160145 - 160
1414chain 'C' and (resid 161 through 174 )CE161 - 174161 - 174
1515chain 'C' and (resid 175 through 189 )CE175 - 189175 - 189
1616chain 'C' and (resid 190 through 205 )CE190 - 205190 - 205
1717chain 'C' and (resid 206 through 220 )CE206 - 220206 - 220

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