[English] 日本語
Yorodumi- PDB-4bot: The structure and super-organization of acetylcholine receptor- r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bot | ||||||
---|---|---|---|---|---|---|---|
Title | The structure and super-organization of acetylcholine receptor- rapsyn complexes class E | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN / NEUROTRANSMITTER RECEPTOR / CLUSTERING / SYNAPSE / NEUROMUSCULAR JUNCTION / NICOTINIC / 43K | ||||||
Function / homology | Function and homology information acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / acetylcholine receptor signaling pathway / transmembrane signaling receptor activity / postsynaptic membrane / neuron projection Similarity search - Function | ||||||
Biological species | TORPEDO MARMORATA (marbled electric ray) | ||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 42 Å | ||||||
Authors | Zuber, B. / Unwin, N. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Structure and superorganization of acetylcholine receptor-rapsyn complexes. Authors: Benoît Zuber / Nigel Unwin / Abstract: The scaffolding protein at the neuromuscular junction, rapsyn, enables clustering of nicotinic acetylcholine receptors in high concentration and is critical for muscle function. Patients with ...The scaffolding protein at the neuromuscular junction, rapsyn, enables clustering of nicotinic acetylcholine receptors in high concentration and is critical for muscle function. Patients with insufficient receptor clustering suffer from muscle weakness. However, the detailed organization of the receptor-rapsyn network is poorly understood: it is unclear whether rapsyn first forms a wide meshwork to which receptors can subsequently dock or whether it only forms short bridges linking receptors together to make a large cluster. Furthermore, the number of rapsyn-binding sites per receptor (a heteropentamer) has been controversial. Here, we show by cryoelectron tomography and subtomogram averaging of Torpedo postsynaptic membrane that receptors are connected by up to three rapsyn bridges, the minimum number required to form a 2D network. Half of the receptors belong to rapsyn-connected groups comprising between two and fourteen receptors. Our results provide a structural basis for explaining the stability and low diffusion of receptors within clusters. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4bot.cif.gz | 341 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bot.ent.gz | 266.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bot_validation.pdf.gz | 606.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bot_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4bot_validation.xml.gz | 118.1 KB | Display | |
Data in CIF | 4bot_validation.cif.gz | 165.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/4bot ftp://data.pdbj.org/pub/pdb/validation_reports/bo/4bot | HTTPS FTP |
-Related structure data
Related structure data | 2383MC 2376C 2377C 2378C 2381C 2382C 4bogC 4boiC 4bonC 4booC 4borC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 52845.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / References: UniProt: P02711 #2: Protein | | Mass: 56123.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / References: UniProt: Q6S3I0 #3: Protein | | Mass: 60017.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / References: UniProt: Q6S3H8 #4: Protein | | Mass: 58118.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / References: UniProt: Q6S3H9 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron tomography |
-Sample preparation
Component | Name: POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN Type: COMPLEX |
---|---|
Buffer solution | Name: 400 MM NACL, 20 MM PHOSPHATE BUFFER, LEUPEPTIN 0.3 MG/L, PEPSTATIN 1 MG/L pH: 7.4 Details: 400 MM NACL, 20 MM PHOSPHATE BUFFER, LEUPEPTIN 0.3 MG/L, PEPSTATIN 1 MG/L |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 78, INSTRUMENT- HOMEMADE PLUNGER, METHOD- BLOT FROM THE CARBON SIDE, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F30 / Date: Jul 25, 2008 / Details: DUAL TILT AXIS TOMOGRAPHY |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 69000 X / Calibrated magnification: 80213 X / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm / Cs: 2 mm |
Specimen holder | Temperature: 85 K / Tilt angle max: 70 ° / Tilt angle min: -70 ° |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 142 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Method: SIMULTANEOUS ITERATIVE RECONSTRUCTION TECHNIQUE (SIRT) Resolution: 42 Å / Num. of particles: 3564 / Nominal pixel size: 7.48 Å / Actual pixel size: 7.48 Å / Magnification calibration: CATALASE CRYSTAL Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2383 (DEPOSITION ID: 11677). Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--ELECTRON MICROSCOPY | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 2BG9 | ||||||||||||||||||||||||
Refinement | Highest resolution: 42 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 42 Å
|