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- EMDB-6207: Structure of 20S supercomplex determined by single particle cryoe... -
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Open data
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Basic information
Entry | Database: EMDB / ID: 6207 |
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Title | Structure of 20S supercomplex determined by single particle cryoelectron microscopy, state II |
![]() | Map of 20S supercomplex, state II. This map is unsharpened and unfiltered. The map was normalized using the program MAPMAN. |
![]() | 20S supercomplex consisting of truncated neuronal SNARE complex, alpha-SNAP, and N-ethylmaleimide sensitive factor (NSF)
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Source | ![]() ![]() ![]() ![]() ![]() |
Method | ![]() ![]() |
![]() | Zhao M / Wu S / Zhou Q / Vivona S / Cipriano DJ / Cheng Y / Brunger AT |
![]() | Journal: Nature / Year: 2015 Title: Mechanistic insights into the recycling machine of the SNARE complex. ![]() |
Validation Report | PDB-ID: 3j97![]() ![]() ![]() |
Date | Deposition: Dec 5, 2014 / Header (metadata) release: Jan 28, 2015 / Map release: Jan 28, 2015 / Last update: Feb 11, 2015 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
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Header (meta data in XML format) | ![]() ![]() ![]() |
Images | ![]() |
Others | ![]() |
FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6207 |
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Links
-Related structure data
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.4312 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire 20S supercomplex consisting of truncated neuronal SNARE complex, ...
+Component #1: protein, N-ethylmaleimide sensitive factor
+Component #2: protein, alpha Soluble NSF Attachment Protein
+Component #3: protein, Syntaxin-1A
+Component #4: protein, Synaptobrevin-2
+Component #5: protein, Synaptosomal-associated protein 25
-Experimental details
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Sample preparation
Specimen | Specimen state: particle / Method: ![]() |
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Sample solution | Specimen conc.: 15 mg/ml Buffer solution: 50 mM Tris-Cl, 150 mM NaCl, 1 mM AMPPNP, 1 mM EDTA, 1 mM DTT, 0.05% v/v Nonident P-40 pH: 8 |
Support film | Holey carbon on top of 400 mesh copper grid |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Blot for 3.5 seconds before plunging. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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![]() | Microscope: FEI POLARA 300 / Date: Jan 28, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 31000 X (nominal) / Cs: 2.3 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: GATAN K2 (4k x 4k) |
-Image acquisition
Image acquisition | Details: Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods. |
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Image processing
![]() | Method: ![]() Details: 3D classification, refinement, and reconstruction were performed using RELION. |
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3D reconstruction | Software: RELION / CTF correction: Each particle / Resolution: 7.8 Å / Resolution method: FSC 0.143, gold-standard |
-Atomic model buiding
Modeling #1 | Software: ![]() Details: D2 domain of NSF was from crystal structure 1NSF. D1 domain of NSF was from related entry EMD-6204. N domain of NSF was from crystal structure 1QCS. aSNAP was a homology model. SNARE complex was from crystal structure 1N7S. Input PDB model: 1NSF Chain ID: A |
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Modeling #2 | Software: ![]() Details: D2 domain of NSF was from crystal structure 1NSF. D1 domain of NSF was from related entry EMD-6204. N domain of NSF was from crystal structure 1QCS. aSNAP was a homology model. SNARE complex was from crystal structure 1N7S. Input PDB model: 1QCS Chain ID: A |
Modeling #3 | Software: ![]() Details: D2 domain of NSF was from crystal structure 1NSF. D1 domain of NSF was from related entry EMD-6204. N domain of NSF was from crystal structure 1QCS. aSNAP was a homology model. SNARE complex was from crystal structure 1N7S. Input PDB model: 1N7S Chain ID: A, B, C, D |
Output model |