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- PDB-8qub: Hexameric HIV-1 CA in complex with DDD00074110 -

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Basic information

Entry
Database: PDB / ID: 8qub
TitleHexameric HIV-1 CA in complex with DDD00074110
ComponentsSpacer peptide 1
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding ...viral budding via host ESCRT complex / host multivesicular body / ISG15 antiviral mechanism / viral nucleocapsid / viral translational frameshifting / 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) / 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 ...Gag protein p6 / Gag protein p6 / : / 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 finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPetit, A.P. / Fyfe, P.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
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. / 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 16, 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
Revision 1.2Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 20, 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: Spacer peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6852
Polymers25,4611
Non-polymers2231
Water3,441191
1
A: Spacer peptide 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,10712
Polymers152,7686
Non-polymers1,3406
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 area15250 Å2
ΔGint-91 kcal/mol
Surface area59610 Å2
Unit cell
Length a, b, c (Å)90.840, 90.840, 56.830
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-WVZ / (1~{S})-1-phenyl-2,4-dihydro-1~{H}-isoquinolin-3-one


Mass: 223.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.63→46.07 Å / Num. obs: 33459 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.29 / Num. unique obs: 1676 / CC1/2: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→46.07 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1609 4.8 %RANDOM
Rwork0.18961 ---
obs0.19063 31848 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.411 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.63→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 17 191 1869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191725
X-RAY DIFFRACTIONr_bond_other_d00.021586
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9732353
X-RAY DIFFRACTIONr_angle_other_deg3.7253.0013692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14925.29468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2715284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.591158
X-RAY DIFFRACTIONr_chiral_restr0.1360.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211912
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02314
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_it3.2873.12879
X-RAY DIFFRACTIONr_mcbond_other3.2843.117878
X-RAY DIFFRACTIONr_mcangle_it4.4584.6711098
X-RAY DIFFRACTIONr_mcangle_other4.4564.6731099
X-RAY DIFFRACTIONr_scbond_it4.3223.406846
X-RAY DIFFRACTIONr_scbond_other4.323.406847
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2634.9651254
X-RAY DIFFRACTIONr_long_range_B_refined7.39538.7132057
X-RAY DIFFRACTIONr_long_range_B_other7.31338.1712009
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 97 -
Rwork0.284 2397 -
obs--100 %

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