[English] 日本語
Yorodumi
- PDB-1r02: Solution structure of Human Orexin-A:Regulator of Appetite and Wa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r02
TitleSolution structure of Human Orexin-A:Regulator of Appetite and Wakefulness
ComponentsOrexin-A
KeywordsNEUROPEPTIDE / turn / helix-loop-helix
Function / homology
Function and homology information


type 1 orexin receptor binding / type 2 orexin receptor binding / negative regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / neuropeptide hormone activity / positive regulation of calcium ion transport / sleep / : ...type 1 orexin receptor binding / type 2 orexin receptor binding / negative regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / neuropeptide hormone activity / positive regulation of calcium ion transport / sleep / : / eating behavior / temperature homeostasis / negative regulation of DNA replication / response to starvation / negative regulation of potassium ion transport / neuropeptide signaling pathway / rough endoplasmic reticulum / excitatory postsynaptic potential / secretory granule / positive regulation of cold-induced thermogenesis / synaptic vesicle / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / chemical synaptic transmission / postsynapse / perinuclear region of cytoplasm / extracellular region
Similarity search - Function
Prepro-orexin / Prepro-orexin
Similarity search - Domain/homology
Hypocretin neuropeptide precursor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsKim, H.-Y. / Hong, E. / Kim, J.-I. / Lee, W.
CitationJournal: J.Biochem.Mol.Biol. / Year: 2004
Title: Solution structure of human orexin-A: regulator of appetite and wakefulness.
Authors: Kim, H.Y. / Hong, E. / Kim, J.I. / Lee, W.
History
DepositionSep 19, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / pdbx_entity_src_syn ...citation / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_DOI / _pdbx_entity_src_syn.details ..._citation.pdbx_database_id_DOI / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Orexin-A


Theoretical massNumber of molelcules
Total (without water)3,5881
Polymers3,5881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3350 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein/peptide Orexin-A / hypocretin-1


Mass: 3588.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43612

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM orexin-A; 50mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
22mM orexin-A; 50mM phosphate buffer; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM K2HPO4 / pH: 7 / Pressure: ambient / Temperature: 278 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerstructure solution
XwinNMR2Brukerprocessing
NMRPipe1.7Delagioprocessing
Sparky3.6Goddarddata analysis
CNS1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR ensembleConformers submitted total number: 1

+
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