[English] 日本語
Yorodumi
- PDB-2jxz: Solution Conformation of A Non-Amyloidogenic Analogue of Human Ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jxz
TitleSolution Conformation of A Non-Amyloidogenic Analogue of Human Calcitonin in Sodium Dodecyl Sulfate Micelles
ComponentsCalcitonin
KeywordsHORMONE / A-HELIX / Amidation / Cleavage on pair of basic residues / Secreted
Function / homology
Function and homology information


artery vasodilation involved in baroreceptor response to increased systemic arterial blood pressure / calcitonin receptor binding / Calcitonin-like ligand receptors / feeding behavior / negative regulation of ossification / negative regulation of bone resorption / negative regulation of smooth muscle contraction / response to pain / neuronal dense core vesicle / activation of protein kinase activity ...artery vasodilation involved in baroreceptor response to increased systemic arterial blood pressure / calcitonin receptor binding / Calcitonin-like ligand receptors / feeding behavior / negative regulation of ossification / negative regulation of bone resorption / negative regulation of smooth muscle contraction / response to pain / neuronal dense core vesicle / activation of protein kinase activity / detection of temperature stimulus involved in sensory perception of pain / monocyte chemotaxis / smooth muscle contraction / neuropeptide signaling pathway / embryo implantation / regulation of cytosolic calcium ion concentration / hippocampal mossy fiber to CA3 synapse / ossification / cellular response to nerve growth factor stimulus / adenylate cyclase-activating G protein-coupled receptor signaling pathway / terminal bouton / hormone activity / cellular response to tumor necrosis factor / positive regulation of cytosolic calcium ion concentration / response to heat / G alpha (s) signalling events / inflammatory response / Amyloid fiber formation / negative regulation of DNA-templated transcription / neuronal cell body / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Calcitonin / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family
Similarity search - Domain/homology
MethodSOLUTION NMR / Restrained Simulated Annealing, Energy Minimization
AuthorsAndreotti, G. / Vitale, R. / Avidan-Shpalter, C. / Amodeo, P. / Gazit, E. / Motta, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Converting the highly amyloidogenic human calcitonin into a powerful fibril inhibitor by 3D structure homology with a non-amyloidogenic analogue
Authors: Andreotti, G. / Vitale, R.M. / Avidan-Shpalter, C. / Amodeo, P. / Gazit, E. / Motta, A.
History
DepositionDec 3, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calcitonin


Theoretical massNumber of molelcules
Total (without water)3,4561
Polymers3,4561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200Restraint violations, Amber energy, Procheck parameters
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Calcitonin /


Mass: 3455.895 Da / Num. of mol.: 1 / Fragment: calcitonin, UNP residues 85-116 / Mutation: Y12L, N17H, A26N, I27T, A31T / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIS / References: UniProt: P01258

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

-
Sample preparation

DetailsContents: 1.5 mM phCalcitonin, 159 mM [U-2H] SDS, 95% H20, 5% D2O
Solvent system: 95% H20, 5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMphCalcitonin1
159 mMSDS[U-2H]1
Sample conditionsIonic strength: 0 / pH: 6.6 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
AMBER6Case, Darden, Cheatham, Simmerling, Wang, Duke, Luo, Kollstructure solution
AMBER6Case, Darden, Cheatham, Simmerling, Wang, Duke, Luo, Kollrefinement
RefinementMethod: Restrained Simulated Annealing, Energy Minimization / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Restraint violations, Amber energy, Procheck parameters
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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