[English] 日本語
Yorodumi
- PDB-1hy9: COCAINE AND AMPHETAMINE REGULATED TRANSCRIPT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hy9
TitleCOCAINE AND AMPHETAMINE REGULATED TRANSCRIPT
ComponentsCOCAINE AND AMPHETAMINE REGULATED TRANSCRIPT PROTEIN
KeywordsSIGNALING PROTEIN / cystEine knot
Function / homology
Function and homology information


somatostatin secretion / positive regulation of epinephrine secretion / : / negative regulation of glucagon secretion / positive regulation of transmission of nerve impulse / adult feeding behavior / negative regulation of appetite / positive regulation of blood pressure / neuropeptide hormone activity / negative regulation of bone resorption ...somatostatin secretion / positive regulation of epinephrine secretion / : / negative regulation of glucagon secretion / positive regulation of transmission of nerve impulse / adult feeding behavior / negative regulation of appetite / positive regulation of blood pressure / neuropeptide hormone activity / negative regulation of bone resorption / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / regulation of insulin secretion / neuropeptide signaling pathway / cellular response to starvation / secretory granule / circadian regulation of gene expression / cell-cell signaling / chemical synaptic transmission / G protein-coupled receptor signaling pathway / synapse / signal transduction / extracellular space
Similarity search - Function
CART, C-terminal domain / CART satiety factor / CART, C-terminal domain superfamily / Cocaine and amphetamine regulated transcript protein (CART) / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Cocaine- and amphetamine-regulated transcript protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulted annealing
AuthorsLudvigsen, S. / Thim, L. / Blom, A.M. / Wulff, B.S.
Citation
Journal: Biochemistry / Year: 2001
Title: Solution structure of the satiety factor, CART, reveals new functionality of a well-known fold.
Authors: Ludvigsen, S. / Thim, L. / Blom, A.M. / Wulff, B.S.
#1: Journal: Nature / Year: 1998
Title: Hypothalamic CART is a New Anorectic Peptide Regulated by Leptin
Authors: Kristensen, P. / Judge, M.E. / Thim, L. / Ribel, U. / Christjansen, K.N. / Wulff, B.S. / Clausen, J.T. / Jensen, P.B. / Madsen, O.D. / Vrang, N. / Larsen, P.J. / Hastrup, S.
#2: Journal: FEBS lett. / Year: 1998
Title: Purification and Characterisation of a New Hypothalamic Satiety Peptide, Cocaine and Amphetamine Regulated Transcript (CART), Produced in Yeast
Authors: Thim, L. / Nielsen, P.F. / Judge, M.E. / Andersen, A.S. / Diers, I. / Egel-Mitani, M. / Hastrup, S.
History
DepositionJan 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COCAINE AND AMPHETAMINE REGULATED TRANSCRIPT PROTEIN


Theoretical massNumber of molelcules
Total (without water)4,3991
Polymers4,3991
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)10 / 100target function
RepresentativeModel #1closest to the average, fewest violations, lowest energy

-
Components

#1: Protein/peptide COCAINE AND AMPHETAMINE REGULATED TRANSCRIPT PROTEIN


Mass: 4399.217 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RESIDUES 76-116)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BRAIN / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q16568

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY

-
Sample preparation

DetailsContents: 1 mM CART / Solvent system: 90% H2O, 10%D2O, pH 6.5
Sample conditionsIonic strength: low / pH: 6.5 / Pressure: 10132 5 / Temperature: 300 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukerprocessing
ProntoKjaer, M.data analysis
MNMR97.2Kjaer, M.processing
X-PLOR3.1Brunger, Astructure solution
VNMR5.3bVariancollection
X-PLOR3.1Brunger, Arefinement
RefinementMethod: distance geometry, simulted annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average, fewest violations, lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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://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