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- PDB-4xrq: Disulfide stabilized HIV-1 CA hexamer 4mut (S41A, Q67H, V165I, L1... -

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Basic information

Entry
Database: PDB / ID: 4xrq
TitleDisulfide stabilized HIV-1 CA hexamer 4mut (S41A, Q67H, V165I, L172I) in complex with PF-3450074
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / capsid / inhibitor
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 / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1B0 / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsPrice, A.J. / James, L.C.
CitationJournal: J.Virol. / Year: 2015
Title: HIV-1 Resistance to the Capsid-Targeting Inhibitor PF74 Results in Altered Dependence on Host Factors Required for Virus Nuclear Entry.
Authors: Zhou, J. / Price, A.J. / Halambage, U.D. / James, L.C. / Aiken, C.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Nov 21, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8952
Polymers25,4691
Non-polymers4261
Water1,67593
1
A: Capsid protein p24
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)155,36912
Polymers152,8166
Non-polymers2,5536
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 area15360 Å2
ΔGint-121 kcal/mol
Surface area59760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.350, 90.350, 56.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Capsid protein p24 / Pr55Gag / CA


Mass: 25469.318 Da / Num. of mol.: 1 / Mutation: A14C,S41A,E45C,Q67H,V165I,L172I,W184A,M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: P12493
#2: Chemical ChemComp-1B0 / N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE


Mass: 425.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M potassium thiocyanate, 8% w/v PEG 20K, 8% v/v PEG 550 MME, 0.1 M TRIS pH 8.5, 3% 1,4-dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→78.245 Å / Num. all: 19460 / Num. obs: 19460 / % possible obs: 100 % / Redundancy: 6.1 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Rsym value: 0.076 / Net I/av σ(I): 8.914 / Net I/σ(I): 15.4 / Num. measured all: 118725
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.0660.6681.21696828420.2990.6682.4100
2.06-2.1860.39421598726570.1750.3944.4100
2.18-2.336.10.2622.91518725080.1160.2626.7100
2.33-2.526.10.1894.11429323380.0830.1899.1100
2.52-2.766.20.1315.81326721550.0570.13113100
2.76-3.086.20.0799.71214919600.0340.07919.5100
3.08-3.566.20.051141081517380.0220.05128.8100
3.56-4.366.20.03917.3910614580.0170.03938.1100
4.36-6.176.20.03220.5717011510.0140.03239.6100
6.17-39.1235.80.02817.637836530.0130.02839.999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.12 Å
Translation2.5 Å39.12 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h47

3h47


Resolution: 1.95→39.12 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2099 / WRfactor Rwork: 0.1767 / FOM work R set: 0.8458 / SU B: 3.448 / SU ML: 0.098 / SU R Cruickshank DPI: 0.148 / SU Rfree: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 995 5.1 %RANDOM
Rwork0.189 18460 --
obs0.1906 18460 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.57 Å2 / Biso mean: 35.385 Å2 / Biso min: 17.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å2-0 Å2
2--0.38 Å20 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.95→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 32 93 1764
Biso mean--37.23 34.73 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191722
X-RAY DIFFRACTIONr_bond_other_d0.0010.021637
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.9772348
X-RAY DIFFRACTIONr_angle_other_deg0.7393.0013768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8345217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6452568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64215280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.902158
X-RAY DIFFRACTIONr_chiral_restr0.0530.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02371
X-RAY DIFFRACTIONr_mcbond_it3.3734.471862
X-RAY DIFFRACTIONr_mcbond_other3.3694.468861
X-RAY DIFFRACTIONr_mcangle_it4.6787.5111075
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 79 -
Rwork0.275 1344 -
all-1423 -
obs--100 %

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