[English] 日本語
Yorodumi
- PDB-1dep: MEMBRANE PROTEIN, NMR, 1 STRUCTURE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dep
TitleMEMBRANE PROTEIN, NMR, 1 STRUCTURE
ComponentsT345-359
KeywordsMEMBRANE PROTEIN / BETA-ADRENOCEPTOR / MICELLE-BOUND PEPTIDE
Function / homology
Function and homology information


beta1-adrenergic receptor activity / positive regulation of heart contraction / regulation of circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of GTPase activity / early endosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
Beta 1 adrenoceptor / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Beta-1 adrenergic receptor
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodSOLUTION NMR
AuthorsJung, H. / Schnackerz, K.D.
Citation
Journal: FEBS Lett. / Year: 1995
Title: NMR and circular dichroism studies of synthetic peptides derived from the third intracellular loop of the beta-adrenoceptor.
Authors: Jung, H. / Windhaber, R. / Palm, D. / Schnackerz, K.D.
#1: Journal: Eur.J.Biochem. / Year: 1991
Title: Multisite Contacts Involved in Coupling of the Beta-Adrenergic Receptor with the Stimulatory Guanine-Nucleotide-Binding Regulatory Protein. Structural and Functional Studies by Beta-Receptor- ...Title: Multisite Contacts Involved in Coupling of the Beta-Adrenergic Receptor with the Stimulatory Guanine-Nucleotide-Binding Regulatory Protein. Structural and Functional Studies by Beta-Receptor-Site-Specific Synthetic Peptides
Authors: Munch, G. / Dees, C. / Hekman, M. / Palm, D.
History
DepositionAug 23, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T345-359


Theoretical massNumber of molelcules
Total (without water)1,8891
Polymers1,8891
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)1 / -
Representative

-
Components

#1: Protein/peptide T345-359


Mass: 1889.294 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PEPTIDE T345-359 REPRESENTS THE FOURTH INTRACELLULAR LOOP OF THE BETA-ADRENOCEPTOR FROM TURKEY
Source: (gene. exp.) Meleagris gallopavo (turkey) / References: UniProt: P07700

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR softwareName: EREF / Developer: JACK,LEVITT / Classification: refinement
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