[English] 日本語
Yorodumi
- PDB-1plp: SOLUTION STRUCTURE OF THE CYTOPLASMIC DOMAIN OF PHOSPHOLAMBAN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1plp
TitleSOLUTION STRUCTURE OF THE CYTOPLASMIC DOMAIN OF PHOSPHOLAMBAN
ComponentsPHOSPHOLAMBAN
KeywordsMEMBRANE PROTEIN / ATPASE / PHOSPHORYLATION / PHOSPHOLAMBAN
Function / homology
Function and homology information


regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of cardiac muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell membrane potential / negative regulation of calcium ion transmembrane transporter activity ...regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of cardiac muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / regulation of cardiac muscle cell membrane potential / negative regulation of calcium ion transmembrane transporter activity / acrosome assembly / negative regulation of calcium ion import / negative regulation of catalytic activity / ATPase inhibitor activity / regulation of the force of heart contraction / negative regulation of ATP-dependent activity / cardiac muscle tissue development / regulation of cardiac muscle cell contraction / blood circulation / enzyme inhibitor activity / relaxation of cardiac muscle / regulation of heart contraction / negative regulation of heart rate / muscle cell cellular homeostasis / regulation of calcium ion transport / Ion transport by P-type ATPases / negative regulation of calcium ion transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Ion homeostasis / Notch signaling pathway / sarcoplasmic reticulum membrane / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum / mitochondrial membrane / intracellular calcium ion homeostasis / ATPase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane
Similarity search - Function
Phospholamban / Phospholamban
Similarity search - Domain/homology
Cardiac phospholamban
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsMortishire-Smith, R.J. / Pitzenberger, S.M. / Burke, C.J. / Middaugh, C.R. / Garsky, V.M. / Johnson, R.G.
CitationJournal: Biochemistry / Year: 1995
Title: Solution structure of the cytoplasmic domain of phopholamban: phosphorylation leads to a local perturbation in secondary structure.
Authors: Mortishire-Smith, R.J. / Pitzenberger, S.M. / Burke, C.J. / Middaugh, C.R. / Garsky, V.M. / Johnson, R.G.
History
DepositionMay 1, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOLAMBAN


Theoretical massNumber of molelcules
Total (without water)2,9011
Polymers2,9011
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)20 / -
Representative

-
Components

#1: Protein/peptide PHOSPHOLAMBAN / PLB(1-25) / ENGINEERED


Mass: 2901.388 Da / Num. of mol.: 1 / Mutation: ARG 25 CYS
Source method: isolated from a genetically manipulated source
Details: NMR, 20 STRUCTURES / Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P26678

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR softwareName: DIANA / Developer: GUNTERT,BRAUN,WUTHRICH / Classification: refinement
NMR ensembleConformers 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://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