[English] 日本語
Yorodumi
- PDB-2mdf: NMR structure of a two-transmembrane segment TM VI-VII of NHE1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mdf
TitleNMR structure of a two-transmembrane segment TM VI-VII of NHE1
ComponentsSodium/hydrogen exchanger 1
KeywordsPROTON TRANSPORT / NHE1 / Na+/H+ exchanger / transmembrane
Function / homology
Function and homology information


cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity / maintenance of cell polarity ...cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / cardiac muscle cell differentiation / sodium ion export across plasma membrane / protein phosphatase 2B binding / response to acidic pH / intracellular sodium ion homeostasis / regulation of stress fiber assembly / cellular response to acidic pH / cardiac muscle cell contraction / sodium ion import across plasma membrane / positive regulation of mitochondrial membrane permeability / regulation of cardiac muscle contraction by calcium ion signaling / regulation of focal adhesion assembly / cellular response to antibiotic / cellular response to cold / positive regulation of cardiac muscle hypertrophy / positive regulation of the force of heart contraction / protein complex oligomerization / intercalated disc / monoatomic ion transport / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / potassium ion transmembrane transport / cellular response to epinephrine stimulus / T-tubule / proton transmembrane transport / regulation of intracellular pH / stem cell differentiation / cellular response to mechanical stimulus / phospholipid binding / cellular response to insulin stimulus / calcium-dependent protein binding / cell migration / lamellipodium / positive regulation of cell growth / protein-macromolecule adaptor activity / basolateral plasma membrane / cellular response to hypoxia / molecular adaptor activity / calmodulin binding / positive regulation of apoptotic process / apical plasma membrane / membrane raft / focal adhesion / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Helix Hairpins - #1330 / Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Sodium/hydrogen exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLee, B.L. / Sykes, B.D. / Alves, C. / Fliegel, L.
CitationJournal: Biochemistry / Year: 2014
Title: Structural and Functional Analysis of the Transmembrane Segment Pair VI and VII of the NHE1 Isoform of the Na(+)/H(+) Exchanger.
Authors: Alves, C. / Lee, B.L. / Sykes, B.D. / Fliegel, L.
History
DepositionSep 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sodium/hydrogen exchanger 1


Theoretical massNumber of molelcules
Total (without water)6,2571
Polymers6,2571
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Sodium/hydrogen exchanger 1 / APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute ...APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1


Mass: 6257.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: P19634

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1412D DQF-COSY
1512D 1H-1H TOCSY
1612D 1H-1H NOESY
1722D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-15N] entity, 5 % [U-2H] D2O, 0.25 mM [1,1,2,2,3,3-2H6] DSS, 95 % H2O, 75-150 mM [U-2H] dodecylphosphocholine, 95% H2O/5% D2O95% H2O/5% D2O
21-2 mM [U-15N] entity, 100 % [U-2H] D2O, 0.25 mM [1,1,2,2,3,3-2H6] DSS, 75-150 mM [U-2H] dodecylphosphocholine, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-15N]1-21
5 %D2O-2[U-2H]1
0.25 mMDSS-3[1,1,2,2,3,3-2H6]1
95 %H2O-41
mMdodecylphosphocholine-5[U-2H]75-1501
mMentity-6[U-15N]1-22
100 %D2O-7[U-2H]2
0.25 mMDSS-8[1,1,2,2,3,3-2H6]2
mMdodecylphosphocholine-9[U-2H]75-1502
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1748 / NOE intraresidue total count: 452 / NOE long range total count: 31 / NOE medium range total count: 389 / NOE sequential total count: 392 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 35 / Protein psi angle constraints total count: 35
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

+
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