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Open data
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Basic information
Entry | Database: PDB / ID: 6eco | ||||||
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Title | Hexamer-2-Foldon HIV-1 capsid platform | ||||||
![]() | (HIV-1 capsid platform protein) x 2 | ||||||
![]() | VIRAL PROTEIN / disulfide / capsid / template-driven polymerization | ||||||
Function / homology | ![]() host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / Budding and maturation of HIV virion / 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Summers, B.J. / Xiong, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Modular HIV-1 Capsid Assemblies Reveal Diverse Host-Capsid Recognition Mechanisms. Authors: Summers, B.J. / Digianantonio, K.M. / Smaga, S.S. / Huang, P.T. / Zhou, K. / Gerber, E.E. / Wang, W. / Xiong, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
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PDB format | ![]() | 123.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ec2C ![]() 6ecnC ![]() 6obhC ![]() 4xfxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 221 / Label seq-ID: 1 - 221
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Components
#1: Protein | Mass: 28129.178 Da / Num. of mol.: 1 / Mutation: E45C, T54E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 24788.379 Da / Num. of mol.: 1 / Mutation: A14C, A42E, A204D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.45 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 0.2M Sodium Chloride, 0.1M HEPES pH 7.5, 12% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→50.01 Å / Num. obs: 8601 / % possible obs: 94.7 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 4.2→4.31 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.815 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XFX Resolution: 4.2→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 375.953 / SU ML: 2.393 / Cross valid method: THROUGHOUT / ESU R Free: 1.13
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 256.555 Å2
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Refinement step | Cycle: 1 / Resolution: 4.2→30 Å
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Refine LS restraints |
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