[English] 日本語
Yorodumi
- PDB-6zbi: Ternary complex of Calmodulin bound to 2 molecules of NHE1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zbi
TitleTernary complex of Calmodulin bound to 2 molecules of NHE1
Components
  • Calmodulin-1
  • Sodium/hydrogen exchanger 1
KeywordsMETAL BINDING PROTEIN / Complex / NHE1 / Calmodulin / Signaling
Function / homology
Function and homology information


Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / cation-transporting ATPase complex / 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 / hyaluronan catabolic process ...Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / cation-transporting ATPase complex / 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 / hyaluronan catabolic process / 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 / intracellular sodium ion homeostasis / regulation of stress fiber assembly / sodium ion import across plasma membrane / positive regulation of mitochondrial membrane permeability / cardiac muscle cell contraction / response to acidic pH / regulation of cardiac muscle contraction by calcium ion signaling / cellular response to acidic pH / CaM pathway / Cam-PDE 1 activation / regulation of focal adhesion assembly / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / cellular response to cold / Activation of RAC1 downstream of NMDARs / positive regulation of cardiac muscle hypertrophy / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / cellular response to antibiotic / positive regulation of the force of heart contraction / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / protein complex oligomerization / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / regulation of ryanodine-sensitive calcium-release channel activity / Ion transport by P-type ATPases / intercalated disc / Uptake and function of anthrax toxins / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Protein methylation / response to muscle stretch / Ion homeostasis / eNOS activation / phosphatidylinositol-4,5-bisphosphate binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / monoatomic ion transport / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / T-tubule / cellular response to epinephrine stimulus / potassium ion transmembrane transport / FCERI mediated Ca+2 mobilization / proton transmembrane transport / calcium channel complex / substantia nigra development / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Ras activation upon Ca2+ influx through NMDA receptor / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
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, transmembrane / EF-hand / : / Recoverin; domain 1 ...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 / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Sodium/hydrogen exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPrestel, A. / Kragelund, B.B. / Pedersen, E.S. / Pedersen, S.F. / Sjoegaard-Frich, L.M.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Danish National Research Foundation4181-00344 Denmark
Novo Nordisk FoundationSYNERGY Denmark
CitationJournal: Elife / Year: 2021
Title: Dynamic Na + /H + exchanger 1 (NHE1) - calmodulin complexes of varying stoichiometry and structure regulate Ca 2+ -dependent NHE1 activation.
Authors: Sjogaard-Frich, L.M. / Prestel, A. / Pedersen, E.S. / Severin, M. / Kristensen, K.K. / Olsen, J.G. / Kragelund, B.B. / Pedersen, S.F.
History
DepositionJun 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin-1
B: Sodium/hydrogen exchanger 1
C: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6927
Polymers25,5313
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3150 Å2
ΔGint-29 kcal/mol
Surface area16290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Calmodulin-1


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pET5 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): codonPlus (DE3)-RP / References: UniProt: P0DP23
#2: Protein/peptide 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: 4405.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: P19634
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-15N NOESY 12C/14N filtered
151isotropic13D 1H-13C NOESY 12C/14N filtered
193isotropic13D 1H-13C NOESY
183isotropic13D 1H-15N NOESY
173isotropic13D 1H-13C NOESY 12C/14N filtered
163isotropic13D 1H-15N NOESY 12C/14N filtered
1101isotropic13D HNCO
1201isotropic13D HN(CA)CB
1191isotropic13D HN(CA)CO
1181isotropic13D C(CO)NH
1171isotropic13D (H)CCH-TOCSY
1161isotropic13D HBHA(CO)NH
1153isotropic13D (H)CCH-TOCSY
1143isotropic13D HBHA(CO)NH
1133isotropic13D HNCO
1123isotropic13D HN(CA)CB
1113isotropic13D CBCA(CO)NH
1213isotropic13D HN(CA)CO
1221isotropic12D 1H-13C HSQC
1231isotropic12D 1H-15N HSQC
1243isotropic12D 1H-13C HSQC
1253isotropic12D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.15 mM Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 95% H2O/5% D2OD95% H2O/5% D2O
solution31 mM [U-99% 13C; U-99% 15N] Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 0.5 mM Calmodulin, 95% H2O/5% D2OE95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCalmodulin[U-99% 13C; U-99% 15N]1
1.15 mMSodium/Hydrogen exchanger 1 (NHE1, SLC9A1)natural abundance1
1 mMSodium/Hydrogen exchanger 1 (NHE1, SLC9A1)[U-99% 13C; U-99% 15N]3
0.5 mMCalmodulinnatural abundance3
Sample conditionsIonic strength: 120 mM / Ionic strength err: 10 / Label: NMR / pH: 7.5 / PH err: 0.2 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 310 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7502

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.44Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin3.5Bruker Biospinprocessing
qMDDKazimierczuk, Orekhovprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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