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- PDB-6omt: HIV-1 capsid hexamer R18D mutant -

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Basic information

Entry
Database: PDB / ID: 6omt
TitleHIV-1 capsid hexamer R18D mutant
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / HIV-1 / capsid / CA
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
Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 Å
AuthorsHuang, P. / Summers, B.J. / Xiong, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)0000-0001-9625-9313 United States
National Science Foundation (NSF, United States)P30GM110758 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM101975 United States
Citation
Journal: Cell Rep / Year: 2019
Title: FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking.
Authors: Huang, P.T. / Summers, B.J. / Xu, C. / Perilla, J.R. / Malikov, V. / Naghavi, M.H. / Xiong, Y.
#1: Journal: Cell Rep / Year: 2019
Title: FEZ1 is recruited to a conserved cofactor site on capsid to promote HIV-1 trafficking
Authors: Huang, P. / Summers, B.J. / Xu, C. / Perilla, J.R. / Malikov, V. / Naghavi, M.H. / Xiong, Y.
History
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)25,5501
Polymers25,5501
Non-polymers00
Water3,927218
1
A: Capsid protein
x 6


Theoretical massNumber of molelcules
Total (without water)153,3026
Polymers153,3026
Non-polymers00
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 area15150 Å2
ΔGint-97 kcal/mol
Surface area61150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.662, 90.662, 56.576
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: 25550.361 Da / Num. of mol.: 1 / Mutation: A14C, E45C, W184A, M185A, R18D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0, UniProt: P12493*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 53.18 %
Crystal growTemperature: 293.15 K / Method: microbatch / Details: 0.1 M Tris-HCl, pH 8.5, 8% PEG8000 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2016
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→45.9 Å / Num. obs: 16794 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.397 / Rmerge(I) obs: 0.126 / Rsym value: 0.134 / Net I/σ(I): 12.2
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.134

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Processing

Software
NameClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.052→45.9 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.54
RfactorNum. reflection% reflection
Rfree0.2212 864 5.18 %
Rwork0.1812 --
obs0.1832 16682 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.052→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 0 218 1899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051730
X-RAY DIFFRACTIONf_angle_d0.9312353
X-RAY DIFFRACTIONf_dihedral_angle_d11.91073
X-RAY DIFFRACTIONf_chiral_restr0.055266
X-RAY DIFFRACTIONf_plane_restr0.005307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0522-2.18080.28631590.26632598X-RAY DIFFRACTION99
2.1808-2.34920.20881410.21252608X-RAY DIFFRACTION100
2.3492-2.58560.22811360.19532635X-RAY DIFFRACTION100
2.5856-2.95970.2291550.18282630X-RAY DIFFRACTION100
2.9597-3.72860.20621390.17142644X-RAY DIFFRACTION100
3.7286-45.91240.21581340.16332703X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.0997 Å / Origin y: 9.3181 Å / Origin z: 0.0035 Å
111213212223313233
T0.2082 Å2-0.0087 Å20.0099 Å2-0.2608 Å2-0.0035 Å2--0.2558 Å2
L0.1299 °2-0.3799 °20.3873 °2-1.0089 °2-0.5969 °2--1.1402 °2
S-0.0015 Å °0.0669 Å °0.0221 Å °-0.0326 Å °-0.0717 Å °-0.1158 Å °0.0023 Å °0.1153 Å °-0 Å °
Refinement TLS groupSelection details: all

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