[English] 日本語
Yorodumi
- PDB-9ps8: Cryo-EM structure of NCLX with calcium (class 2a) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ps8
TitleCryo-EM structure of NCLX with calcium (class 2a)
ComponentsNCLX
KeywordsMEMBRANE PROTEIN / Membrane transporter
Function / homology
Function and homology information


calcium:sodium antiporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of lymphocyte chemotaxis / Mitochondrial calcium ion transport / Sodium/Calcium exchangers / calcium export from the mitochondrion / calcium:sodium antiporter activity / mitochondrial calcium ion transmembrane transport / regulation of cardiac muscle cell membrane potential / mitochondrial calcium ion homeostasis / regulation of store-operated calcium entry ...calcium:sodium antiporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of lymphocyte chemotaxis / Mitochondrial calcium ion transport / Sodium/Calcium exchangers / calcium export from the mitochondrion / calcium:sodium antiporter activity / mitochondrial calcium ion transmembrane transport / regulation of cardiac muscle cell membrane potential / mitochondrial calcium ion homeostasis / regulation of store-operated calcium entry / mitochondrial crista / regulation of cytosolic calcium ion concentration / sodium ion transmembrane transport / regulation of insulin secretion / sarcolemma / mitochondrial membrane / calcium ion transmembrane transport / intracellular calcium ion homeostasis / glucose homeostasis / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein
Similarity search - Domain/homology
Mitochondrial sodium/calcium exchanger protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsZhang, J. / Feng, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
The G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: Nature / Year: 2025
Title: Structure and mechanism of the mitochondrial calcium transporter NCLX
Authors: Fan, M. / Tsai, C.-W. / Zhang, J. / Zhang, J. / Krishnan, A.R. / Liu, T.-Y. / Huang, Y.-L. / Aydin, D. / Du, S. / Sobecks, B.L. / Rodriguez, M.X. / Reiter, A.H. / Bertozzi, C.R. / Dror, R.O. ...Authors: Fan, M. / Tsai, C.-W. / Zhang, J. / Zhang, J. / Krishnan, A.R. / Liu, T.-Y. / Huang, Y.-L. / Aydin, D. / Du, S. / Sobecks, B.L. / Rodriguez, M.X. / Reiter, A.H. / Bertozzi, C.R. / Dror, R.O. / Tsai, M.-F. / Feng, L.
History
DepositionJul 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NCLX
B: NCLX
C: NCLX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,2336
Polymers192,1133
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein NCLX / Mitochondrial sodium/calcium exchanger protein / Na(+)/K(+)/Ca(2+)-exchange protein 6 / ...Mitochondrial sodium/calcium exchanger protein / Na(+)/K(+)/Ca(2+)-exchange protein 6 / Sodium/calcium exchanger protein / mitochondrial / Sodium/potassium/calcium exchanger 6 / Solute carrier family 24 member 6 / Solute carrier family 8 member B1


Mass: 64037.688 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc8b1, Nckx6, Nclx, Slc24a6 / Production host: Homo sapiens (human) / References: UniProt: Q6AXS0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: NCLX without Calcium / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Rattus norvegicus (Norway rat)10116
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameCategory
1Topazparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145777 / Symmetry type: POINT
RefinementHighest resolution: 2.97 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211641
ELECTRON MICROSCOPYf_angle_d0.60115911
ELECTRON MICROSCOPYf_dihedral_angle_d3.7561570
ELECTRON MICROSCOPYf_chiral_restr0.0381936
ELECTRON MICROSCOPYf_plane_restr0.0041935

+
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