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- PDB-1eq8: THREE-DIMENSIONAL STRUCTURE OF THE PENTAMERIC HELICAL BUNDLE OF T... -

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Basic information

Entry
Database: PDB / ID: 1eq8
TitleTHREE-DIMENSIONAL STRUCTURE OF THE PENTAMERIC HELICAL BUNDLE OF THE ACETYLCHOLINE RECEPTOR M2 TRANSMEMBRANE SEGMENT
ComponentsACETYLCHOLINE RECEPTOR PROTEIN
KeywordsSIGNALING PROTEIN / NEUROTRANSMITTER RECEPTOR / M2 / LIPID BILAYERS / ION-CHANNEL / HELICAL BUNDLE / PENTAMERIC BUNDLE
Function / homology
Function and homology information


acetylcholine-gated monoatomic cation-selective channel activity / 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 delta
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodSOLID-STATE NMR / X-PLOR 3.1, distance geometry, simulated annealing, molecular dynamics, FISI, FINGERPRINT, HOLE
AuthorsMarassi, F.M. / Gesell, J.J. / Kim, Y. / Valente, A.P. / Oblatt-Montal, M. / Montal, M. / Opella, S.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy.
Authors: Opella, S.J. / Marassi, F.M. / Gesell, J.J. / Valente, A.P. / Kim, Y. / Oblatt-Montal, M. / Montal, M.
#1: Journal: J.BIOMOL.NMR / Year: 1999
Title: Dilute Spin-Exchange Assignment of Solid-State NMR Spectra of Oriented Proteins: Acetylcholine M2 in Bilayers
Authors: Marassi, F.M. / Gesell, J.J. / Valente, A.P. / Kim, Y. / Oblatt-Montal, M. / Montal, M. / Opella, S.J.
History
DepositionApr 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Sep 25, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conf / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINE RECEPTOR PROTEIN
B: ACETYLCHOLINE RECEPTOR PROTEIN
C: ACETYLCHOLINE RECEPTOR PROTEIN
D: ACETYLCHOLINE RECEPTOR PROTEIN
E: ACETYLCHOLINE RECEPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,6105
Polymers12,6105
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 30structures with favorable non-bond energy
Representativeminimized average structure

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Components

#1: Protein/peptide
ACETYLCHOLINE RECEPTOR PROTEIN / ACHR M2


Mass: 2522.013 Da / Num. of mol.: 5 / Fragment: M2 SEGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Torpedo californica (Pacific electric ray)
Cell: NEURON / Cellular location: POST-SYNAPTIC MEMBRANE / Organ: BRAIN / Plasmid: PMAL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02718

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC; HNCA; HN(CO)CA; 3D 15N- and 13C-edited NOESY; 3D 15N- and 13C-edited TOCSY; 3D HNHA
2221D CPMOIST; 2D 1H/1H-15N PISEMA; 2D 1H/15N HETCOR;
NMR detailsText: The orientation of each monomer in the pentameric bundle was obtained from the combination of the solution NMR (PDB file 1a11) and solid-state NMR (PDB file 1cek) structures

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM M2 U-15N; 350mM DPC; pH5.5;90% H2O/10% D2O
220mg M2 U-15N; 40mg DMPC;DMPC bilayers in H2O;
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.5ambient 303 K
25.5ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX6002
Chemagnetics CMXChemagneticsCMX4003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.01Brungerrefinement
FISI1.01Marassistructure solution
HOLESmart, Goodfellow, Wallacestructure solution
Felix95data analysis
RefinementMethod: X-PLOR 3.1, distance geometry, simulated annealing, molecular dynamics, FISI, FINGERPRINT, HOLE
Software ordinal: 1
Details: The backbone coordinates obtained from solution NMR were superimposed on the coordinates obtained from solid-state NMR to fix the helix orientation and rotation in the membrane. The ...Details: The backbone coordinates obtained from solution NMR were superimposed on the coordinates obtained from solid-state NMR to fix the helix orientation and rotation in the membrane. The pentameric array was then optimized using molecular dynamics. Pore contours were calculated with the program HOLE.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 30 / Conformers submitted total number: 1

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