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- PDB-7rmj: Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhi... -

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Basic information

Entry
Database: PDB / ID: 7rmj
TitleDisulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor (S)-N-(1-(3-(4-chloro-3-(methylsulfonamido)-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-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide
ComponentsCAPSID PROTEIN P24
KeywordsVIRAL PROTEIN / inhibitor
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
Chem-61F / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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)U54 AI150472 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143649 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 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 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 / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 9, 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

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)80,42428
Polymers76,3843
Non-polymers4,04025
Water3,963220
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)160,57951
Polymers152,7686
Non-polymers7,81245
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)161,38566
Polymers152,7686
Non-polymers8,61860
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)160.023, 160.023, 57.598
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 8...
d_2ens_1(chain "B" and (resid 1 through 5 or resid 8...
d_3ens_1(chain "C" and (resid 1 through 5 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROASNA1 - 5
d_12ens_1GLYPROA8 - 99
d_13ens_1GLYLEUA101 - 111
d_14ens_1GLULYSA113 - 131
d_15ens_1TRPVALA134 - 143
d_16ens_1METALAA145 - 175
d_17ens_1GLNGLNA177
d_18ens_1GLNGLNA180
d_19ens_1VALGLUA182 - 188
d_110ens_1LEUVALA190 - 192
d_111ens_1ASNLEUA194 - 203
d_112ens_1ALALEUA205 - 212
d_113ens_1GLUGLNA214 - 220
d_21ens_1PROASND1 - 5
d_22ens_1GLYPROD8 - 99
d_23ens_1GLYLEUD102 - 112
d_24ens_1GLULYSD114 - 132
d_25ens_1TRPVALD134 - 143
d_26ens_1METALAD145 - 175
d_27ens_1GLNGLND177 - 178
d_28ens_1VALGLUD180 - 186
d_29ens_1LEUVALD188 - 190
d_210ens_1ASNLEUD192 - 201
d_211ens_1ALALEUD203 - 210
d_212ens_1GLUGLND213 - 219
d_31ens_1PROASNG1 - 5
d_32ens_1GLYPROG8 - 99
d_33ens_1GLYLEUG101 - 111
d_34ens_1GLULYSG113 - 131
d_35ens_1TRPVALG133 - 142
d_36ens_1METALAG144 - 174
d_37ens_1GLNGLNG176
d_38ens_1GLNGLNG179
d_39ens_1VALGLUG181 - 187
d_310ens_1LEUVALG189 - 191
d_311ens_1ASNLEUG193 - 202
d_312ens_1ALALEUG204 - 211
d_313ens_1GLUGLNG213 - 219

NCS oper:
IDCodeMatrixVector
1given(-0.999858356918, -0.0131684167771, -0.0104813596809), (0.0132275220325, -0.999896887661, -0.00558987539989), (-0.0104066691144, -0.00572772604882, 0.999929444707)159.083514214, -93.5768238142, 0.538925416648
2given(0.0289686200384, -0.999580282461, 0.000279226236817), (-0.999562469942, -0.0289697710337, -0.00596833720869), (0.00597392131304, -0.000106209574086, -0.999982150333)-48.4271298552, 78.5462234979, 26.7823185096

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Components

#1: Protein CAPSID PROTEIN P24


Mass: 25461.271 Da / Num. of mol.: 3 / Mutation: A14C, E45C, 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-61F / N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetamide


Mass: 934.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H36ClF8N7O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 55.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.125M NaI, 4.5% Peg 3350, 6% glycerol, 0.1M sodium cacodylate 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: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 39080 / % possible obs: 99.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 29.56 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.8
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1866 / CC1/2: 0.601 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VKV

6vkv


Resolution: 2.27→44.29 Å / SU ML: 0.2718 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 1892 4.84 %
Rwork0.2139 37167 -
obs0.2156 39059 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.51 Å2
Refinement stepCycle: LAST / Resolution: 2.27→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 208 220 5481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00265599
X-RAY DIFFRACTIONf_angle_d0.63697702
X-RAY DIFFRACTIONf_chiral_restr0.041805
X-RAY DIFFRACTIONf_plane_restr0.0045957
X-RAY DIFFRACTIONf_dihedral_angle_d14.76122051
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.594288204853
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.463969339515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.32551390.27952559X-RAY DIFFRACTION96.43
2.33-2.390.28131340.25942618X-RAY DIFFRACTION99.49
2.39-2.460.29161420.25292647X-RAY DIFFRACTION100
2.46-2.540.28221540.2442611X-RAY DIFFRACTION100
2.54-2.630.27041350.25052640X-RAY DIFFRACTION100
2.63-2.740.28691020.24512683X-RAY DIFFRACTION99.96
2.74-2.860.28821590.24182633X-RAY DIFFRACTION99.93
2.86-3.010.31241290.22872639X-RAY DIFFRACTION99.96
3.01-3.20.26811250.22952673X-RAY DIFFRACTION100
3.2-3.450.24891490.21442637X-RAY DIFFRACTION100
3.45-3.80.23311230.18522685X-RAY DIFFRACTION99.93
3.8-4.340.21441190.17072690X-RAY DIFFRACTION99.96
4.34-5.470.20181400.17852695X-RAY DIFFRACTION99.96
5.47-44.290.19761420.21682757X-RAY DIFFRACTION99.55
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)
12.25661275132-0.5807149157780.02437297706032.07507364279-0.5230127109532.09027417214-0.007918132897210.1686707798140.0581158922288-0.249147096995-0.09346950621430.0188121750550.1586872284210.1188447882410.07576704131030.211778471518-0.0113011438263-0.02013784880750.1739094806460.001152028470010.19622228634496.741-65.229-6.132
22.54150759751.18977134977-0.3343346220992.17187395075-0.8350690418663.042516922510.016974232995-0.371588099863-0.07479529092960.40711218789-0.25017633202-0.312638444724-0.2445474558510.3019405079330.1273026619160.3255677681140.02925305837420.015782051620.2635413436140.02207840084080.24034003872878.97-80.10818.431
32.02464434826-0.1214974718621.207489438651.78751573388-0.3118988357161.34055959469-0.01284080312120.143050898571-0.362896792978-0.04670737371880.1309860790290.07660449897150.346840853928-0.0118523714579-0.03792312457560.429531032933-0.01255634958460.06145689895170.267976077347-0.02842607647070.29840362979378.142-83.49611.365
41.634387446310.06575368043730.8535056549820.8695569097660.2603576829381.74975946132-0.06398591667340.0556646510278-0.0547468067511-0.176128395587-0.04534747103450.026140158341-0.143315343917-0.01029971830810.09365239954020.2625950104910.01486227648660.03201035337040.245400519812-0.003627050875240.24444967251364.716-25.535-3.404
52.561003212671.19282825782-0.9658972041543.372007075370.8636235664482.62395847182-0.164180176817-0.1674678394960.289838779169-0.110561703930.1792511430790.044981843109-0.6295731213890.0934633159616-0.006213019382240.3970556345850.00907173645109-0.049711100270.270683429481-0.02126442276010.24845755800687.49-7.44715.145
61.49775156234-0.201250530841-0.2205524313351.58118334928-0.3941503371362.24014391811-0.0343597355065-0.1742530884040.008687487551760.0598249299182-0.01845615197460.03959556875240.009940595720990.1775271851730.05869079557210.1449662079130.00195261766769-0.006152241269240.180202419741-0.04227447119960.19310011091419.577-16.2633.38
73.080960640152.24211671291-0.3236798793452.831411736620.9378589759633.08138704579-0.1893811522950.140771824819-0.303596366647-0.1233453157330.262373810456-0.3445116272770.2360917913240.258521216792-0.02560377311480.2126408835360.009845544016470.036019615590.220165846809-0.01283746663330.23474123264438.1075.88111.363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:144 )A1 - 144
2X-RAY DIFFRACTION2( CHAIN A AND RESID 145:174 )A145 - 174
3X-RAY DIFFRACTION3( CHAIN A AND RESID 175:219 )A175 - 219
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:160 )B1 - 160
5X-RAY DIFFRACTION5( CHAIN B AND RESID 161:220 )B161 - 220
6X-RAY DIFFRACTION6( CHAIN C AND RESID 1:144 )C1 - 144
7X-RAY DIFFRACTION7( CHAIN C AND RESID 145:220 )C145 - 220

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