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- PDB-9s6w: HIV-1 capsid (M-group) - native in complex with JW3-100 -

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Basic information

Entry
Database: PDB / ID: 9s6w
TitleHIV-1 capsid (M-group) - native in complex with JW3-100
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / Hexameric HIV-1 (M-group)
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
: / 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 ...: / 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.
Similarity search - Domain/homology
Chem-1PG / : / BETA-MERCAPTOETHANOL / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.074 Å
AuthorsGovasli, M.A.L. / Pinotsis, N. / Towers, G. / Selwood, D. / Jacques, D.A.
Funding support United Kingdom, European Union, Australia, 4items
OrganizationGrant numberCountry
Wellcome Trust220863 United Kingdom
Wellcome Trust214344 United Kingdom
European Research Council (ERC)339223European Union
National Health and Medical Research Council (NHMRC, Australia)GNT2013215 Australia
CitationJournal: To Be Published
Title: Cofactor-mimicking HIV-1 capsid inhibitors, and their escape mutants, drive innate immune sensing
Authors: Govasli, M.A.L. / Pinotsis, N. / Towers, G. / Selwood, D. / Jacques, D.A.
History
DepositionAug 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,93210
Polymers25,6301
Non-polymers1,3029
Water1,44180
1
A: Gag polyprotein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,59360
Polymers153,7836
Non-polymers7,81054
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 area24280 Å2
ΔGint-380 kcal/mol
Surface area63560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.88, 92.88, 57.61
Angle α, β, γ (deg.)90, 90, 120
Int Tables number168
Space group name H-MP6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gag polyprotein


Mass: 25630.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0

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Non-polymers , 6 types, 89 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#6: Chemical ChemComp-A1JL5 / (S)-N-(1-(5-((2-amino-2-oxoethyl)thio)-4-(4-(tert-Butyl)phenyl)-4H-1,2,4-triazol-3-yl)-2-(3,5-difluorophenyl)ethyl)-2-(5-hydroxy-1H-indol-3-yl)acetamide / ~{N}-[(1~{S})-2-[3,5-bis(fluoranyl)phenyl]-1-[4-(4-~{tert}-butylphenyl)-5-methylsulfanyl-1,2,4-triazol-3-yl]ethyl]-2-(5-oxidanyl-1~{H}-indol-3-yl)ethanamide


Mass: 575.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H31F2N5O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9.5-11% PEG 3350 (v/v), 250-350 mM NaI, 100 mM Sodium Cacodylate [pH 6.5]. Crystals grew in 1 uL protein (3 mg/mL) + 1 uL crystallant. Cryoprotected in 20% (v/v) Glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.07→80.44 Å / Num. obs: 13593 / % possible obs: 78.4 % / Redundancy: 27.5 % / CC1/2: 0.999 / Net I/σ(I): 0.133
Reflection shellResolution: 2.07→2.19 Å / Num. unique obs: 675 / CC1/2: 0.49

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
STARANISO2.3.28 (20200301)data scaling
XDSJan 31, 2020 (BUILT 20200131)data reduction
PHASER2.8.3phasing
autoPROC1.0.5 (20200319)data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.074→80.44 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.871 / SU R Cruickshank DPI: 0.326 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.326 / SU Rfree Blow DPI: 0.245 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.2979 639 -RANDOM
Rwork0.2626 ---
obs0.2642 13593 78.4 %-
Displacement parametersBiso mean: 64.13 Å2
Baniso -1Baniso -2Baniso -3
1--3.7945 Å20 Å20 Å2
2---3.7945 Å20 Å2
3---7.5891 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.074→80.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 62 80 1855
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0061832HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.842492HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d630SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes305HARMONIC5
X-RAY DIFFRACTIONt_it1832HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion240SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1534SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion18
LS refinement shellResolution: 2.074→2.16 Å
RfactorNum. reflection% reflection
Rfree0.2546 20 -
Rwork0.2145 --
obs--21.51 %
Refinement TLS params.

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)
1-0.02240.49060.42813.438-0.81940-0.06030.3307-0.3050.3307-0.0507-0.197-0.305-0.1970.1109-0.1131-0.0465-0.0323-0.11880.10160.2004-0.3347-16.89642.7853
20.89370.2531-0.99070.299-0.29876.25110.02740.2514-0.10290.25140.30130.3147-0.10290.3147-0.3287-0.01960.09470.0856-0.18760.08910.0983-3.1672-31.164912.3456
32.18571.2359-0.92240.69850.5742.2156-0.0546-0.16970.205-0.16970.02770.17160.2050.17160.027-0.08570.0744-0.0887-0.09750.03840.079626.5089-28.4734-13.6484
45.23142.6013-1.40298.5389-3.36683.43010.39490.07060.11030.0706-0.3804-0.17780.1103-0.1778-0.0145-0.2503-0.0171-0.0503-0.07490.14460.2158-10.1627-28.76170.4525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|62}A1 - 62
2X-RAY DIFFRACTION2{ A|63 - A|142}A63 - 142
3X-RAY DIFFRACTION3{ A|143 - A|221}A143 - 221
4X-RAY DIFFRACTION4{ A|309 - A|309}A309

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