[English] 日本語
Yorodumi
- PDB-2moa: Solution NMR structure of peptide ImI1 (peak 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2moa
TitleSolution NMR structure of peptide ImI1 (peak 2)
ComponentsAlpha-conotoxin ImI
KeywordsTOXIN / dithiol amino acid / conotoxin / bicyclic peptide / macrocycle / phage display
Function / homologyConotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region / Alpha-conotoxin ImI mutant / Alpha-conotoxin ImI
Function and homology information
Biological speciesConus imperialis (invertebrata)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model1
AuthorsHeinis, C. / Chen, S.
Citation
Journal: Nat Chem / Year: 2014
Title: Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides.
Authors: Chen, S. / Gopalakrishnan, R. / Schaer, T. / Marger, F. / Hovius, R. / Bertrand, D. / Pojer, F. / Heinis, C.
#1: Journal: J.Med.Chem. / Year: 1999
Title: Solution structure of alpha-conotoxin ImI by 1H nuclear magnetic resonance.
Authors: Gehrmann, J. / Daly, N.L. / Alewood, P.F. / Craik, D.J.
#2: Journal: Febs Lett. / Year: 1999
Title: NMR spatial structure of alpha-conotoxin ImI reveals a common scaffold in snail and snake toxins recognizing neuronal nicotinic acetylcholine receptors.
Authors: Maslennikov, I.V. / Shenkarev, Z.O. / Zhmak, M.N. / Ivanov, V.T. / Methfessel, C. / Tsetlin, V.I. / Arseniev, A.S.
#3: Journal: Biochemistry / Year: 1999
Title: NMR solution structure of alpha-conotoxin ImI and comparison to other conotoxins specific for neuronal nicotinic acetylcholine receptors.
Authors: Rogers, J.P. / Luginbuhl, P. / Shen, G.S. / McCabe, R.T. / Stevens, R.C. / Wemmer, D.E.
#4: Journal: Febs Lett. / Year: 1999
Title: Minimal conformation of the alpha-conotoxin ImI for the alpha7 neuronal nicotinic acetylcholine receptor recognition: correlated CD, NMR and binding studies.
Authors: Lamthanh, H. / Jegou-Matheron, C. / Servent, D. / Menez, A. / Lancelin, J.M.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural determinants of selective alpha-conotoxin binding to a nicotinic acetylcholine receptor homolog AChBP.
Authors: Ulens, C. / Hogg, R.C. / Celie, P.H. / Bertrand, D. / Tsetlin, V. / Smit, A.B. / Sixma, T.K.
History
DepositionApr 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-conotoxin ImI


Theoretical massNumber of molelcules
Total (without water)1,3851
Polymers1,3851
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)20 / 50target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Alpha-conotoxin ImI / Alpha-CTx ImI


Type: Cyclic peptide / Class: Toxin / Mass: 1384.654 Da / Num. of mol.: 1 / Fragment: UNP residues 5-16 / Mutation: C2(81S), C3A / Source method: obtained synthetically / Source: (synth.) Conus imperialis (invertebrata) / References: UniProt: P50983, Alpha-conotoxin ImI mutant

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Bicyclic peptide ImI1 (peak 2) was generated by substituing two adjacent cysteines in ImI with a dithiol amino acid 1a.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

-
Sample preparation

DetailsContents: 1 mM ImI1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: ImI1-1
Sample conditionsIonic strength: 0.1 / pH: 5.8 / Pressure: ambient / Temperature: 278 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Sparky3.113Goddardchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
ProcheckNMRLaskowski and MacArthurdata analysis
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 163 / NOE intraresidue total count: 107 / NOE long range total count: 3 / NOE medium range total count: 11 / NOE sequential total count: 42
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.143 Å
NMR ensemble rmsDistance rms dev: 0.071 Å / Distance rms dev error: 0.023 Å

+
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://pdbjlvh1.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