[English] 日本語
Yorodumi
- PDB-2kb7: Hybrid solution and solid-state NMR structure of monomeric phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kb7
TitleHybrid solution and solid-state NMR structure of monomeric phospholamban in lipid bilayers
ComponentsPhospholamban
KeywordsMEMBRANE PROTEIN / phospholamban / PISEMA / hybrid method / lipid bilayers / topology
Function / homology
Function and homology information


negative regulation of calcium ion binding / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / acrosome assembly / negative regulation of calcium ion transmembrane transporter activity ...negative regulation of calcium ion binding / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / acrosome assembly / negative regulation of calcium ion transmembrane transporter activity / negative regulation of catalytic activity / negative regulation of calcium ion import / ATPase inhibitor activity / regulation of cardiac muscle cell contraction / cardiac muscle tissue development / negative regulation of heart rate / muscle cell cellular homeostasis / locomotor rhythm / enzyme inhibitor activity / regulation of calcium ion transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Notch signaling pathway / sarcoplasmic reticulum membrane / mitochondrial membrane / visual learning / intracellular calcium ion homeostasis / ATPase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / identical protein binding
Similarity search - Function
Phospholamban / Phospholamban / Phospholamban / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SOLID-STATE NMR / simulated annealing
AuthorsTraaseth, N.J. / Shi, L. / Verardi, R. / Veglia, G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach.
Authors: Traaseth, N.J. / Shi, L. / Verardi, R. / Mullen, D.G. / Barany, G. / Veglia, G.
#1: Journal: J.Biomol.Nmr / Year: 2009
Title: A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints.
Authors: Shi, L. / Traaseth, N.J. / Verardi, R. / Cembran, A. / Gao, J. / Veglia, G.
History
DepositionNov 21, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: Phospholamban


Theoretical massNumber of molelcules
Total (without water)6,1501
Polymers6,1501
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Phospholamban


Mass: 6150.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Bl21de3phi / Gene: pln / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / References: UniProt: P61015*PLUS

-
Experimental details

-
Experiment

Experiment
Method
SOLUTION NMR
SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D H(CCO)NH
1313D C(CO)NH
1413D 1H-15N NOESY
2522D [1H,15N] PISEMA
2622D [1H,15N]SAMPI4

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 15N] and [U-99% 13C; U-99% 15N] Phospholamban, 90% H2O/10% D2O90% H2O/10% D2O
2160/1 lipid/protein (mol/mol) [U-99% 15N] and [15N-Ala] and [15N-Arg] and [15N-Asn] and [15N-Ile] and [15N-Met] and [15N-Leu] and [15N-Phe] and [15N-Val] and [15N-Ser] and [15N-Gln26,Gln29] Phospholamban, 100% H2O100% H2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingSolution-ID
1.5 mMPhospholamban[U-99% 15N] and [U-99% 13C; U-99% 15N]1
%Phospholamban[U-99% 15N] and [15N-Ala] and [15N-Arg] and [15N-Asn] and [15N-Ile] and [15N-Met] and [15N-Leu] and [15N-Phe] and [15N-Val] and [15N-Ser] and [15N-Gln26,Gln29]2
Sample conditionspH: 6 / Pressure: ambient / Temperature units: K

-
Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian VNMRSVarianVNMRS7002
Bruker DMXBrukerDMX6003

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18Schwieters, C. et al.refinement
X-PLOR NIH2.18Schwieters, C. et al.data analysis
X-PLOR NIH2.18Schwieters, C. et al.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Authors state that they define the z-axis to be parallel with the bilayer normal. Also, the origin (or in other words, when the z Cartesian coordinate is 0) is defined to be the center of the lipid bilayer.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers 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://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