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- PDB-6mqo: Structure of HIV-1 CA G208R -

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Basic information

Entry
Database: PDB / ID: 6mqo
TitleStructure of HIV-1 CA G208R
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...viral budding via host ESCRT complex / viral process / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell cytoplasm / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane / cytoplasm
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 / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSmaga, S.S. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082251-12 United States
CitationJournal: Structure / Year: 2019
Title: MxB Restricts HIV-1 by Targeting the Tri-hexamer Interface of the Viral Capsid.
Authors: Smaga, S.S. / Xu, C. / Summers, B.J. / Digianantonio, K.M. / Perilla, J.R. / Xiong, Y.
History
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 20, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1163
Polymers25,8621
Non-polymers2542
Water724
1
A: Capsid protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,69318
Polymers155,1716
Non-polymers1,52312
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 area15750 Å2
ΔGint-86 kcal/mol
Surface area63970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.970, 91.970, 57.121
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 Capsid protein / Capsid


Mass: 25861.766 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: G208R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 15% PEG3350, 0.1 M sodium iodide, Bis-Tris propane, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2016
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 4626 / % possible obs: 97.4 % / Redundancy: 2.65 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.31
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1671 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XFX

4xfx


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.86 / SU B: 51.366 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27132 251 5.5 %RANDOM
Rwork0.20578 ---
obs0.20903 4353 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.361 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0.68 Å20 Å2
2---1.35 Å20 Å2
3---4.39 Å2
Refinement stepCycle: 1 / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 2 4 1693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191726
X-RAY DIFFRACTIONr_bond_other_d0.0020.021664
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9572346
X-RAY DIFFRACTIONr_angle_other_deg1.06633836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90124.59574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44615298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2241511
X-RAY DIFFRACTIONr_chiral_restr0.1280.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
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_it3.6385.54862
X-RAY DIFFRACTIONr_mcbond_other3.6395.537861
X-RAY DIFFRACTIONr_mcangle_it5.8788.2981074
X-RAY DIFFRACTIONr_mcangle_other5.8758.3021075
X-RAY DIFFRACTIONr_scbond_it3.6175.94864
X-RAY DIFFRACTIONr_scbond_other3.6155.942865
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1298.7721273
X-RAY DIFFRACTIONr_long_range_B_refined10.27952.2667139
X-RAY DIFFRACTIONr_long_range_B_other10.27852.2697140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 18 -
Rwork0.294 301 -
obs--99.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3720.188-1.21074.59490.6676.7039-0.23610.38870.2314-0.6906-0.22730.36110.0415-0.11580.46340.12110.0077-0.02330.0573-0.03880.26561.5118-25.7155-7.8044
26.6464-1.8112-1.67056.48920.41443.493-0.1151-0.4605-0.3640.41040.17680.48950.0972-0.5185-0.06170.2485-0.1138-0.0070.23660.02820.1872-27.8641-28.099312.5816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION2A147 - 255

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