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- PDB-8qv4: Hexameric HIV-1 CA in complex with DDD01728503 -

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Basic information

Entry
Database: PDB / ID: 8qv4
TitleHexameric HIV-1 CA in complex with DDD01728503
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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. / 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
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 1.3Oct 23, 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

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Assembly

Deposited unit
A: Spacer peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8204
Polymers25,4611
Non-polymers3583
Water1,15364
1
A: Spacer peptide 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)154,91824
Polymers152,7686
Non-polymers2,15018
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 area17070 Å2
ΔGint-62 kcal/mol
Surface area60900 Å2
Unit cell
Length a, b, c (Å)90.399, 90.399, 56.654
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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-WZX / ethyl 2-(3-oxidanylidene-2,4-dihydroquinoxalin-1-yl)ethanoate


Mass: 234.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
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: 1.5418 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: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→28.33 Å / Num. obs: 7164 / % possible obs: 97.7 % / Redundancy: 6 % / CC1/2: 0.96 / Rmerge(I) obs: 0.3 / Net I/σ(I): 4.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1046 / CC1/2: 0.67 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→28.33 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.835 / SU B: 15.68 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30264 332 4.6 %RANDOM
Rwork0.22975 ---
obs0.23305 6827 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å20 Å2
2--0.43 Å20 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 2.7→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 25 64 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131741
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171624
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.672362
X-RAY DIFFRACTIONr_angle_other_deg1.2111.5783787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96223.21484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3771510
X-RAY DIFFRACTIONr_chiral_restr0.0680.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
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_it2.3563.26862
X-RAY DIFFRACTIONr_mcbond_other2.3523.259861
X-RAY DIFFRACTIONr_mcangle_it3.8344.8781074
X-RAY DIFFRACTIONr_mcangle_other3.8334.881075
X-RAY DIFFRACTIONr_scbond_it2.1573.379879
X-RAY DIFFRACTIONr_scbond_other2.1553.377880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6324.9881289
X-RAY DIFFRACTIONr_long_range_B_refined7.79558.6857212
X-RAY DIFFRACTIONr_long_range_B_other7.79758.7637193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 22 -
Rwork0.369 494 -
obs--98.29 %

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