- PDB-2kbv: Structural and functional analysis of TM XI of the NHE1 isoform o... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2kbv
Title
Structural and functional analysis of TM XI of the NHE1 isoform of thE NA+/H+ exchanger
Components
Sodium/hydrogen exchanger 1
Keywords
MEMBRANE PROTEIN / transmembrane / NHE1 / micelle / Alternative splicing / Antiport / Glycoprotein / Ion transport / Membrane / Phosphoprotein / Sodium / Sodium transport / Transport
Function / homology
Function and homology information
sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / sodium:proton antiporter activity ...sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / sodium:proton antiporter activity / positive regulation of action potential / maintenance of cell polarity / positive regulation of calcineurin-NFAT signaling cascade / regulation of pH / sodium ion export across plasma membrane / cardiac muscle cell differentiation / cellular response to acidic pH / sodium ion import across plasma membrane / protein phosphatase 2B binding / intracellular sodium ion homeostasis / response to acidic pH / regulation of stress fiber assembly / cardiac muscle cell contraction / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of mitochondrial membrane permeability / cellular response to cold / cellular response to antibiotic / regulation of focal adhesion assembly / positive regulation of cardiac muscle hypertrophy / positive regulation of the force of heart contraction / cellular response to organic cyclic compound / intercalated disc / monoatomic ion transport / potassium ion transmembrane transport / T-tubule / cellular response to epinephrine stimulus / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / proton transmembrane transport / stem cell differentiation / regulation of intracellular pH / cellular response to mechanical stimulus / cellular response to insulin stimulus / phospholipid binding / calcium-dependent protein binding / cell migration / lamellipodium / protein complex oligomerization / cellular response to hypoxia / positive regulation of cell growth / protein-macromolecule adaptor activity / basolateral plasma membrane / molecular adaptor activity / calmodulin binding / apical plasma membrane / membrane raft / positive regulation of apoptotic process / 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
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 family Similarity search - Domain/homology
Sodium/hydrogenexchanger1 / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1 / Na(+)/H(+) antiporter / ...Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1 / Na(+)/H(+) antiporter / amiloride-sensitive / APNH
Mass: 2886.417 Da / Num. of mol.: 1 / Fragment: NHE1 transmembrane segment XI / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19634
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D DQF-COSY
1
2
1
2D 1H-1H TOCSY
1
3
1
2D 1H-1H NOESY
1
4
1
2D 1H-13C HSQC
-
Sample preparation
Details
Contents: 150 mM DPC-1, 0.25 mM DSS-2, 2 mM TMXI-3, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)
Component
Solution-ID
150mM
DPC-1
1
0.25mM
DSS-2
1
2mM
TMXI-3
1
Sample conditions
pH: 5 / Pressure: ambient / Temperature: 303 K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
800
1
Varian INOVA
Varian
INOVA
500
2
Varian INOVA
Varian
INOVA
600
3
-
Processing
NMR software
Name
Version
Developer
Classification
X-PLOR NIH
2.19
Schwieters, Kuszewski, TjandraandClore
structuresolution
X-PLOR NIH
2.19
Schwieters, Kuszewski, TjandraandClore
refinement
VnmrJ
Varian
collection
NMRView
Johnson, OneMoonScientific
processing
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
Refinement
Method: simulated annealing / Software ordinal: 1 Details: 10 rounds of simulated annealing and restraint refinement, followed by further rounds of refinment including dihedral angle restraints.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 40
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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