[English] 日本語
Yorodumi
- PDB-1go9: Monitoring the structural Consequences of Phe12-->D-Phe12 and Leu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1go9
TitleMonitoring the structural Consequences of Phe12-->D-Phe12 and Leu15-->Aib15 substitution in h/r Corticotropin Releasing Hormone: Implications for Design of CRH antagonists.
ComponentsCORTICOTROPIN RELEASING HORMONE
KeywordsHORMONE / CORTICOTROPIN RELEASING HORMONE / SYNTHETIC ANALOGUES / SOLID PHASE SYNTHESIS / SOLUTIONS STRUCTURE
Function / homology
Function and homology information


corticotropin-releasing hormone activity / positive regulation of digestive system process / positive regulation of corticosterone secretion / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of circadian sleep/wake cycle, REM sleep / corticotropin-releasing hormone receptor 2 binding / positive regulation of corticotropin secretion / positive regulation of cortisol secretion / regulation of serotonin secretion / negative regulation of glucagon secretion ...corticotropin-releasing hormone activity / positive regulation of digestive system process / positive regulation of corticosterone secretion / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of circadian sleep/wake cycle, REM sleep / corticotropin-releasing hormone receptor 2 binding / positive regulation of corticotropin secretion / positive regulation of cortisol secretion / regulation of serotonin secretion / negative regulation of glucagon secretion / MECP2 regulates transcription of neuronal ligands / positive regulation of behavioral fear response / glucocorticoid biosynthetic process / negative regulation of norepinephrine secretion / parturition / hormone-mediated apoptotic signaling pathway / negative regulation of luteinizing hormone secretion / monoatomic ion homeostasis / negative regulation of epinephrine secretion / varicosity / positive regulation of cAMP-mediated signaling / response to ether / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / synaptic transmission, dopaminergic / negative regulation of systemic arterial blood pressure / regulation of NMDA receptor activity / Class B/2 (Secretin family receptors) / cellular response to cocaine / diterpenoid metabolic process / adrenal gland development / response to corticosterone / response to aldosterone / hypothalamus development / response to pain / positive regulation of calcium ion import / locomotory exploration behavior / positive regulation of insulin secretion involved in cellular response to glucose stimulus / associative learning / response to immobilization stress / cellular response to dexamethasone stimulus / female pregnancy / long-term synaptic potentiation / lung development / hormone activity / response to estrogen / G alpha (s) signalling events / chemical synaptic transmission / perikaryon / neuron apoptotic process / response to ethanol / learning or memory / inflammatory response / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of gene expression / signaling receptor binding / positive regulation of cell population proliferation / synapse / positive regulation of gene expression / signal transduction / extracellular space / extracellular region
Similarity search - Function
Urocortin/corticotropin-releasing factor / Corticotropin-releasing factor conserved site / Corticotropin-releasing factor family signature. / corticotropin-releasing factor / Corticotropin-releasing factor / Corticotropin-releasing factor family
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY SIMULATED ANNEALING IN TORSION ANGLE SPACE
Model type detailsMINIMIZED AVERAGE
AuthorsSpyroulias, G.A. / Papazacharias, S. / Pairas, G. / Cordopatis, P.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Monitoring the Structural Consequences of Phe12-->D-Phe and Leu15-->Aib Substitution in Human/Rat Corticotropin Releasing Hormone. Implications for Design of Crh Antagonists.
Authors: Spyroulias, G.A. / Papazacharias, S. / Pairas, G. / Cordopatis, P.
#1: Journal: Protein Eng. / Year: 1993
Title: Solution Structure of Human Corticotropin Releasing Factor by 1H NMR and Distance Geometry with Restrained Molecular Dynamics.
Authors: Romier, C. / Bernassau, J.M. / Cambillau, C. / Darbon, H.
History
DepositionOct 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CORTICOTROPIN RELEASING HORMONE


Theoretical massNumber of molelcules
Total (without water)4,7341
Polymers4,7341
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)1 / 40LEAST RESTRAINT VIOLATION
Representative

-
Components

#1: Protein/peptide CORTICOTROPIN RELEASING HORMONE / CORTICOLIBERIN


Mass: 4734.436 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically
Details: SYNTHETIC ANALOGUE SYNTHESIZED THROUGH SOLID PHASE SYNTHESIS USING FMOC/TBU SYNTHETIC PROTOCOLS. NATIVE PHE12 AND LEU15 HAS BEEN SUBSTITUTED BY D-PHE AND ALPHA-AMINOISOBUTYRIC ACID
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P06850

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY
NMR detailsText: MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING 1H-1H DOUBLE-RESONANCE NMR SPECTROSCOPY. NMR-DERRIVED DISTANCE RESTRAINTS AND 3JHAHN COUPLING CONSTANTS AS WELL AS H-BOND CONSTRAINTS USED IN ...Text: MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING 1H-1H DOUBLE-RESONANCE NMR SPECTROSCOPY. NMR-DERRIVED DISTANCE RESTRAINTS AND 3JHAHN COUPLING CONSTANTS AS WELL AS H-BOND CONSTRAINTS USED IN STRUCTURAL CALCULATION AND REFIMENT PROCEEDURE.

-
Sample preparation

DetailsContents: 34% H2O / 66% TFE
Sample conditionspH: 3.8 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
AMBER5PETER KOLLMAN, DAVE CASE, KEN MERZ, THOMAS CHEATHAM, CARLOS SIMMERLING, TOM DARDENrefinement
DYANAstructure solution
AMBERstructure solution
RefinementMethod: HYBRID DISTANCE GEOMETRY SIMULATED ANNEALING IN TORSION ANGLE SPACE
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 40 / Conformers 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