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- PDB-9s6o: HIV-1 capsid (M-group) - native in complex with JW3-076 -

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Basic information

Entry
Database: PDB / ID: 9s6o
TitleHIV-1 capsid (M-group) - native in complex with JW3-076
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / Hexameric HIV-1 (M-group)
Function / homology
Function and homology information


host multivesicular body / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / 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
: / BETA-MERCAPTOETHANOL / IODIDE ION / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.089 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 1.0Aug 12, 2026Provider: 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)26,5969
Polymers25,6301
Non-polymers9658
Water86548
1
A: Gag polyprotein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)159,57454
Polymers153,7836
Non-polymers5,79248
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 area24230 Å2
ΔGint-374 kcal/mol
Surface area61700 Å2
Unit cell
Length a, b, c (Å)92.71, 92.71, 57.36
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 , 5 types, 56 molecules

#2: Chemical ChemComp-A1JL3 / (2~{S})-3-[3,5-difluorophenyl)ethyl]-~{N}-(4-methoxyphenyl)-~{N}-methyl-2-[2-(2-methyl-1~{H}-indol-3-yl)ethanoylamino]propanamide / (2~{S})-3-[3,5-bis(fluoranyl)phenyl]-~{N}-(4-methoxyphenyl)-~{N}-methyl-2-[2-(2-methyl-1~{H}-indol-3-yl)ethanoylamino]propanamide


Mass: 491.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27F2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IOD / IODIDE ION


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


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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
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: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.09→57.36 Å / Num. obs: 12829 / % possible obs: 76.3 % / Redundancy: 19.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.7
Reflection shellResolution: 2.09→2.23 Å / Num. unique obs: 643 / CC1/2: 0.356

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSJan 31, 2020 (BUILT 20200131)data reduction
XSCALEJan 31, 2020 (BUILT 20200131)data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.089→57.36 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.292 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.213
RfactorNum. reflection% reflectionSelection details
Rfree0.249 643 -RANDOM
Rwork0.224 ---
obs0.2253 12829 76.2 %-
Displacement parametersBiso mean: 70.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.5952 Å20 Å20 Å2
2---2.5952 Å20 Å2
3---5.1903 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.089→57.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 46 48 1811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0151810HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.352462HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d623SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes303HARMONIC5
X-RAY DIFFRACTIONt_it1810HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion238SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1479SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion19.34
LS refinement shellResolution: 2.09→2.19 Å
RfactorNum. reflection% reflection
Rfree0.2136 19 -
Rwork0.2255 --
obs0.2249 401 18.25 %
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)
12.9921-1.0408-0.66161.23280.8830-0.16370.1340.15740.1340.05910.27070.15740.27070.1046-0.11520.01750.0936-0.1841-0.00840.0511-14.53688.63113.5953
20.3521-0.36780.02790.67391.43366.96090.03390.00590.02420.00590.2338-0.06740.0242-0.0674-0.2677-0.22120.01840.0573-0.0911-0.0458-0.0298-25.528418.658612.7057
31.03390.32290.10851.68010.53762.38750.1353-0.06410.0552-0.0641-0.1104-0.47140.0552-0.4714-0.025-0.2152-0.03670.0176-0.00910.0088-0.0903-37.9278-8.7756-13.1391
42.1037-1.2665-1.8672-1.9238-2.58688.3155-0.33240.0103-0.36020.01030.4869-0.4645-0.3602-0.4645-0.1545-0.1337-0.00890.0737-0.1763-0.10460.0897-19.972322.91190.1872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|62}
2X-RAY DIFFRACTION2{ A|63 - A|142}
3X-RAY DIFFRACTION3{ A|143 - A|221}
4X-RAY DIFFRACTION4{ A|601 - A|601}

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