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- PDB-7m9f: Structure of the wild-type native full-length HIV-1 capsid protei... -

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Basic information

Entry
Database: PDB / ID: 7m9f
TitleStructure of the wild-type native full-length HIV-1 capsid protein in complex with ZW-1261
ComponentsHIV-1 capsid protein
KeywordsVIRAL PROTEIN / HIV-1 capsid protein / hexamer / CA-targeting antiviral
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
IODIDE ION / Chem-YTG / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsKirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120860 United States
CitationJournal: Viruses / Year: 2021
Title: Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation.
Authors: Sun, Q. / Levy, R.M. / Kirby, K.A. / Wang, Z. / Sarafianos, S.G. / Deng, N.
History
DepositionMar 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7277
Polymers25,6301
Non-polymers1,0966
Water81145
1
A: HIV-1 capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)160,36142
Polymers153,7836
Non-polymers6,57936
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 area19070 Å2
ΔGint-94 kcal/mol
Surface area64080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.900, 90.900, 56.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein HIV-1 capsid protein


Mass: 25630.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL4-3 / Gene: Gag-pol / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12493
#2: Chemical ChemComp-YTG / N-(4-chlorophenyl)-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-methyl-L-phenylalaninamide


Mass: 461.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H24ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.61 Å3/Da / Density % sol: 52.92 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, NaI, Sodium Cacodylate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.71 Å / Num. obs: 7239 / % possible obs: 97.9 % / Redundancy: 7.208 % / Biso Wilson estimate: 69.356 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.118 / Χ2: 0.899 / Net I/σ(I): 13.62 / Num. measured all: 52178 / Scaling rejects: 79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.776.0640.7683.3930445515020.7830.8491.1
2.77-2.857.6180.74.9140305305290.7990.75499.8
2.85-2.937.5530.5925.8138825145140.860.64100
2.93-3.027.6510.5246.8537494914900.8820.56799.8
3.02-3.127.4870.418.4537365004990.9180.44799.8
3.12-3.237.5660.3349.8334884614610.8880.365100
3.23-3.357.3710.26711.3333394544530.9290.29199.8
3.35-3.497.2790.18613.1931084314270.9460.20499.1
3.49-3.647.0070.14515.129014164140.980.15899.5
3.64-3.826.7860.11915.8727014003980.9730.13299.5
3.82-4.036.0530.10415.3821853733610.980.11596.8
4.03-4.277.3910.08919.1827203713680.9920.09799.2
4.27-4.577.4570.08321.1724163313240.9920.08997.9
4.57-4.937.5510.07322.6623713183140.9940.07898.7
4.93-5.47.2570.07921.5921192962920.9920.08598.6
5.4-6.047.2660.07821.6219112692630.9920.08497.8
6.04-6.987.0090.0722.6916052372290.990.07696.6
6.98-8.546.3110.05826.4411361961800.9960.06391.8
8.54-12.087.8290.05133.1611901651520.9990.05592.1
12.08-45.717.9280.05833.754794690.9990.06273.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.27 Å32.23 Å
Translation5.27 Å32.23 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSJan 31, 2020data reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XFZ

4xfz


Resolution: 2.7→45.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2617 / WRfactor Rwork: 0.1769 / FOM work R set: 0.7808 / SU B: 32.491 / SU ML: 0.306 / SU R Cruickshank DPI: 0.2804 / SU Rfree: 0.3594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 356 4.9 %RANDOM
Rwork0.1686 ---
obs0.1728 6881 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178 Å2 / Biso mean: 70.635 Å2 / Biso min: 33.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å2-0 Å2
2---0.36 Å20 Å2
3---1.16 Å2
Refinement stepCycle: final / Resolution: 2.7→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 38 45 1808
Biso mean--55.32 71.02 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191801
X-RAY DIFFRACTIONr_bond_other_d0.0020.021664
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.9762449
X-RAY DIFFRACTIONr_angle_other_deg1.3713.0043878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73525.06577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88315307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4291510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211975
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02335
X-RAY DIFFRACTIONr_rigid_bond_restr4.97831801
X-RAY DIFFRACTIONr_sphericity_free93.97151
X-RAY DIFFRACTIONr_sphericity_bonded20.04651762
LS refinement shellResolution: 2.702→2.772 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 18 -
Rwork0.239 476 -
all-494 -
obs--91.31 %
Refinement TLS params.Method: refined / Origin x: 8.1945 Å / Origin y: -26.3649 Å / Origin z: -0.233 Å
111213212223313233
T0.0322 Å20.0039 Å2-0.005 Å2-0.0275 Å20.0007 Å2--0.0069 Å2
L0.4439 °20.0185 °2-0.0044 °2-0.1258 °20.0075 °2--0.0012 °2
S0.0017 Å °0.0386 Å °0.0141 Å °-0.0057 Å °-0.0009 Å °-0.0251 Å °-0.0015 Å °-0.0045 Å °-0.0008 Å °

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