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- PDB-4bog: The structure and super-organization of acetylcholine receptor-ra... -

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Basic information

Entry
Database: PDB / ID: 4bog
TitleThe structure and super-organization of acetylcholine receptor-rapsyn complexes
Components
  • Acetylcholine receptor beta subunit
  • Acetylcholine receptor delta subunit
  • Acetylcholine receptor gamma subunit
  • Acetylcholine receptor subunit alpha
KeywordsTRANSPORT PROTEIN / CLUSTERING / SYNAPSE / NEUROMUSCULAR JUNCTION / NICOTINIC / RAPSYN / 43K / ELECTRIC ORGAN
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
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Acetylcholine receptor delta subunit / Acetylcholine receptor gamma subunit / Acetylcholine receptor beta subunit
Similarity search - Component
Biological speciesTorpedo marmorata (marbled electric ray)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 50 Å
AuthorsZuber, B. / Unwin, N.
CitationJournal: 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
DepositionMay 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3Sep 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: cell / entity ...cell / entity / entity_src_nat / pdbx_validate_symm_contact / struct_ref
Item: _cell.length_a / _cell.length_b ..._cell.length_a / _cell.length_b / _cell.length_c / _entity.pdbx_description / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-2376
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  • Superimposition on EM map
  • EMDB-2376
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
0: Acetylcholine receptor beta subunit
1: Acetylcholine receptor delta subunit
2: Acetylcholine receptor subunit alpha
3: Acetylcholine receptor gamma subunit
A: Acetylcholine receptor subunit alpha
B: Acetylcholine receptor beta subunit
C: Acetylcholine receptor delta subunit
D: Acetylcholine receptor subunit alpha
E: Acetylcholine receptor gamma subunit
F: Acetylcholine receptor subunit alpha
G: Acetylcholine receptor beta subunit
H: Acetylcholine receptor delta subunit
I: Acetylcholine receptor subunit alpha
J: Acetylcholine receptor gamma subunit
K: Acetylcholine receptor subunit alpha
L: Acetylcholine receptor beta subunit
M: Acetylcholine receptor delta subunit
N: Acetylcholine receptor subunit alpha
O: Acetylcholine receptor gamma subunit
P: Acetylcholine receptor subunit alpha
Q: Acetylcholine receptor beta subunit
R: Acetylcholine receptor delta subunit
S: Acetylcholine receptor subunit alpha
T: Acetylcholine receptor gamma subunit
U: Acetylcholine receptor subunit alpha
V: Acetylcholine receptor beta subunit
W: Acetylcholine receptor delta subunit
X: Acetylcholine receptor subunit alpha
Y: Acetylcholine receptor gamma subunit
Z: Acetylcholine receptor subunit alpha


Theoretical massNumber of molelcules
Total (without water)1,679,70230
Polymers1,679,70230
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
Acetylcholine receptor beta subunit


Mass: 56123.594 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Torpedo marmorata (marbled electric ray) / Cell: ELECTROCYTE / Cellular location: POSTSYNAPTIC PLASMA MEMBRANE / References: UniProt: Q6S3I0
#2: Protein
Acetylcholine receptor delta subunit


Mass: 60017.684 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Torpedo marmorata (marbled electric ray) / Cell: ELECTROCYTE / Cellular location: POSTSYNAPTIC PLASMA MEMBRANE / References: UniProt: Q6S3H8
#3: Protein
Acetylcholine receptor subunit alpha


Mass: 52845.523 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Torpedo marmorata (marbled electric ray) / Cell: ELECTROCYTE / Cellular location: POSTSYNAPTIC PLASMA MEMBRANE / References: UniProt: P02711
#4: Protein
Acetylcholine receptor gamma subunit


Mass: 58118.012 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Torpedo marmorata (marbled electric ray) / Cell: ELECTROCYTE / Cellular location: POSTSYNAPTIC PLASMA MEMBRANE / References: UniProt: Q6S3H9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: ACETYLCHOLINE RECEPTOR- RAPSYN COMPLEX / Type: COMPLEX
Buffer solutionName: 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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jul 25, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 69000 X / Calibrated magnification: 80213 X / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm / Cs: 2 mm
Specimen holderTemperature: 85 K / Tilt angle max: 70 ° / Tilt angle min: -70 °
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 142

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Processing

EM software
IDNameCategoryDetails
1UCSF Chimeramodel fitting
2IMOD3D reconstruction
3PRIISM/IVE3D reconstruction
4TOMO3D3D reconstruction
5Xmipp3D reconstructionML
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MAXIMUM LIKELIHOOD SUBTOMOGRAM AVERAGING / Resolution: 50 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-2376. (DEPOSITION ID: 11658).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--ELECTRON MICROSCOPY
Atomic model buildingPDB-ID: 2BG9

2bg9


Accession code: 2BG9 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 50 Å
Refinement stepCycle: LAST / Highest resolution: 50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms89544 0 0 0 89544

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