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- PDB-8qux: Hexameric HIV-1 CA in complex with DDD00100333 -

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Basic information

Entry
Database: PDB / ID: 8qux
TitleHexameric HIV-1 CA in complex with DDD00100333
ComponentsSpacer peptide 1
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
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
4-benzyl-3,4-dihydroquinoxalin-2(1H)-one / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPetit, A.P. / Fyfe, P.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Chemmedchem / Year: 2024
Title: Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments.
Authors: Lang, S. / Fletcher, D.A. / Petit, A.P. / Luise, N. / Fyfe, P.K. / Zuccotto, F. / Porter, D. / Hope, A. / Bellany, F. / Kerr, C. / MacKenzie, C.J. / Wyatt, P.G. / Gray, D.W.
#1: Journal: Biorxiv / Year: 2023
Title: Application of an NMR/crystallography fragment screening platform for the assessment and rapid discovery of new HIV-CA binding fragments
Authors: Lang, S. / Fletcher, D.A. / Petit, A.P. / Luise, N. / Fyfe, P.K. / Zuccotto, F. / Porter, D. / Hope, D. / Bellany, F. / Kerr, C. / MacKenzie, C.J. / Wyatt, P. / Gray, D.W.
History
DepositionOct 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spacer peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8244
Polymers25,4611
Non-polymers3623
Water2,414134
1
A: Spacer peptide 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,94224
Polymers152,7686
Non-polymers2,17518
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 area17410 Å2
ΔGint-50 kcal/mol
Surface area61050 Å2
Unit cell
Length a, b, c (Å)90.392, 90.392, 56.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Spacer peptide 1 / SP1 / p2


Mass: 25461.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P12493
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-S0I / 4-benzyl-3,4-dihydroquinoxalin-2(1H)-one


Mass: 238.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris buffer, pH 8.0 to 9.0, 10-15% PEG550MME, 0.15M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→28.33 Å / Num. obs: 11849 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.22 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1717 / CC1/2: 0.68 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.878 / SU B: 8.308 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27553 563 4.8 %RANDOM
Rwork0.20131 ---
obs0.20478 11279 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 2.3→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 26 134 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171632
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.6712387
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5783808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.6935.546229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77123.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44315293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.561159
X-RAY DIFFRACTIONr_chiral_restr0.0670.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3853.376872
X-RAY DIFFRACTIONr_mcbond_other2.3663.373871
X-RAY DIFFRACTIONr_mcangle_it3.8195.0521090
X-RAY DIFFRACTIONr_mcangle_other3.8195.0551091
X-RAY DIFFRACTIONr_scbond_it2.463.621885
X-RAY DIFFRACTIONr_scbond_other2.4593.621886
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0575.3161297
X-RAY DIFFRACTIONr_long_range_B_refined6.340.8062104
X-RAY DIFFRACTIONr_long_range_B_other6.25340.7282076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 36 -
Rwork0.254 837 -
obs--99.89 %

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