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- PDB-9mla: Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9mla | |||||||||||||||||||||||||||
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Title | Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab | |||||||||||||||||||||||||||
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![]() | VIRAL PROTEIN / Human endogenous retrovirus K / glycoprotein / HERV-K / envelope / pre-fusion / Fab complex | |||||||||||||||||||||||||||
Function / homology | ![]() | |||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å | |||||||||||||||||||||||||||
![]() | Shek, J. / Sun, C. / Hastie, K. / Saphire, E.O. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Human endogenous retrovirus HERV-K envelope glycoprotein structures in pre- and post-fusion conformations by cryo-EM Authors: Shek, J. / Sun, C. / Hastie, K. / Saphire, E.O. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 466.5 KB | Display | ![]() |
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PDB format | ![]() | 384.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 77.6 KB | Display | |
Data in CIF | ![]() | 117.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 48351MC ![]() 9mlkC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 42193.434 Da / Num. of mol.: 3 / Mutation: V437C, S463R, K464R, Source method: isolated from a genetically manipulated source Details: Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V437C mutation Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 27455.500 Da / Num. of mol.: 3 / Mutation: V498C Source method: isolated from a genetically manipulated source Details: Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V498C mutation. Fusion protein with enterokinase site, GGS linkers, and T4-fibritin foldon trimerization domain. C- ...Details: Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V498C mutation. Fusion protein with enterokinase site, GGS linkers, and T4-fibritin foldon trimerization domain. C-terminal HRV-3C protease site and twin-strep II tag. Source: (gene. exp.) ![]() ![]() Gene: ERVK-25 / Cell line (production host): S2 / Production host: ![]() ![]() |
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-Antibody , 2 types, 6 molecules GHIJKL
#3: Antibody | Mass: 13437.055 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Cleaved Fabs / Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Antibody | Mass: 11671.895 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 5 types, 30 molecules 
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 / Details: Filtered and degassed | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.179 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: GRAPHENE OXIDE / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15947 |
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Processing
EM software | Name: PHENIX / Version: 1.21.1_5286: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 479625 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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