[English] 日本語
Yorodumi
- PDB-1kc4: NMR Structural Analysis of the Complex Formed Between alpha-Bunga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kc4
TitleNMR Structural Analysis of the Complex Formed Between alpha-Bungarotoxin and the Principal alpha-Neurotoxin Binding Sequence on the alpha7 Subunit of a Neuronal Nicotinic Acetylcholine Receptor
Components
  • alpha-bungarotoxin
  • neuronal acetylcholine receptor protein, alpha-7 chain
KeywordsTOXIN / alpha-bungarotoxin / nicotinic acetylcholine receptor alpha 7 subunit / alpha-neurotoxin / ligand-gated ion channels / protein-protein interactions / protein-peptide complex
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / acetylcholine binding / chloride channel regulator activity / synaptic transmission, cholinergic / negative regulation of tumor necrosis factor production / toxic substance binding ...acetylcholine receptor activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / acetylcholine binding / chloride channel regulator activity / synaptic transmission, cholinergic / negative regulation of tumor necrosis factor production / toxic substance binding / negative regulation of cytokine production involved in inflammatory response / regulation of membrane potential / response to nicotine / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / amyloid-beta binding / toxin activity / monoatomic ion transmembrane transport / chemical synaptic transmission / perikaryon / postsynaptic membrane / response to hypoxia / positive regulation of MAPK cascade / neuron projection / axon / positive regulation of cell population proliferation / synapse / dendrite / signal transduction / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / Nicotinic acetylcholine receptor / CD59 / CD59 / Snake toxin-like superfamily ...Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / Nicotinic acetylcholine receptor / CD59 / CD59 / Snake toxin-like superfamily / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Neuronal acetylcholine receptor subunit alpha-7 / Alpha-bungarotoxin
Similarity search - Component
Biological speciesGallus gallus (chicken)
Bungarus multicinctus (many-banded krait)
MethodSOLUTION NMR / distance geometry dynamical simulated annealing
AuthorsMoise, L. / Piserchio, A. / Basus, V.J. / Hawrot, E.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: NMR structural analysis of alpha-bungarotoxin and its complex with the principal alpha-neurotoxin-binding sequence on the alpha 7 subunit of a neuronal nicotinic acetylcholine receptor.
Authors: Moise, L. / Piserchio, A. / Basus, V.J. / Hawrot, E.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Chimeric analysis of a neuronal nicotinic acetylcholine receptor reveals amino acids conferring sensitivity to alpha-bungarotoxin.
Authors: Levandoski, M.M. / Lin, Y. / Moise, L. / McLaughlin, J.T. / Cooper, E. / Hawrot, E.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Identification of sequence segments forming the alpha-bungarotoxin binding sites on two nicotinic acetylcholine receptor alpha subunits from the avian brain.
Authors: McLane, K.E. / Wu, X.D. / Schoepfer, R. / Lindstrom, J.M. / Conti-Tronconi, B.M.
#3: Journal: Biochemistry / Year: 1988
Title: Structural studies of alpha-bungarotoxin. 1. Sequence-specific 1H NMR resonance assignments.
Authors: Basus, V.J. / Billeter, M. / Love, R.A. / Stroud, R.M. / Kuntz, I.D.
History
DepositionNov 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha-bungarotoxin
B: neuronal acetylcholine receptor protein, alpha-7 chain


Theoretical massNumber of molelcules
Total (without water)10,3542
Polymers10,3542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -The submitted conformer models are the 10 with the lowest energy from a pool of over 100 accepted structures that had no restraint violations.
RepresentativeModel #1determined by nmrclust 1.2

-
Components

#1: Protein alpha-bungarotoxin / long neurotoxin 1


Mass: 8005.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60615
#2: Protein/peptide neuronal acetylcholine receptor protein, alpha-7 chain


Mass: 2348.629 Da / Num. of mol.: 1 / Fragment: alpha-neurotoxin binding site
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET31b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)pLysS / References: UniProt: P22770

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
1413D 15N-separated TOCSY
1512D 1H-15N HSQC
161HNHA
NMR detailsText: THE WELL-DEFINED REGIONS IN THE COMPLEX, EXHIBITING EXTENSIVE LONG RANGE NOES, ARE: BGTX: 1-16, 22-28, 39-48, AND 54-68 ALPHA 7 19MER: 185-194

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM alpha-bungarotoxin/[U-15N]-alpha 7 19mer complex 30 mM sodium phosphate, pH 5.5 50 micromolar sodium azide 50 micromolar TMSP95% H2O/5% D2O
21.6 mM alpha-bungarotoxin/[U-15N]-alpha 7 19mer complex 30 mM sodium phosphate, pH 5.5 50 micromolar sodium azide 50 micromolar TMSP99.9% D2O
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE4002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1collection
NMRPipe1.8Delaglio, F., et al.processing
Sparky3.87Goddard, T.D. and Kneller, D.G.data analysis
CNS1Brunger, A.T., et al.refinement
RefinementMethod: distance geometry dynamical simulated annealing / Software ordinal: 1
Details: RMS DEVIATIONS FROM IDEAL VALUES: BOND LENGTH(A) 0.0039, ANGLES(DEG) 0.61, IMPROPERS(DEG) 0.53
NMR representativeSelection criteria: determined by nmrclust 1.2
NMR ensembleConformer selection criteria: The submitted conformer models are the 10 with the lowest energy from a pool of over 100 accepted structures that had no restraint violations.
Conformers submitted total number: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more