[English] 日本語
Yorodumi
- EMDB-13163: Cryo EM structure of bison NHA2 in nano disc structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13163
TitleCryo EM structure of bison NHA2 in nano disc structure
Map data
Sample
  • Complex: detergent structure
    • Protein or peptide: mitochondrial sodium/hydrogen exchanger 9B2
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Phosphatidylinositol
Function / homology
Function and homology information


lithium ion transport / lithium:proton antiporter activity / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / sodium ion transport / mitochondrial membrane / synaptic vesicle membrane / recycling endosome / recycling endosome membrane ...lithium ion transport / lithium:proton antiporter activity / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / sodium ion transport / mitochondrial membrane / synaptic vesicle membrane / recycling endosome / recycling endosome membrane / basolateral plasma membrane / endosome membrane / apical plasma membrane / lysosomal membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9B2
Similarity search - Component
Biological speciesBison bison (American bison)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsMatsuoka R / Fudim R / Jung S / Drew D
Funding support1 items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Nat Struct Mol Biol / Year: 2022
Title: Structure, mechanism and lipid-mediated remodeling of the mammalian Na/H exchanger NHA2.
Authors: Rei Matsuoka / Roman Fudim / Sukkyeong Jung / Chenou Zhang / Andre Bazzone / Yurie Chatzikyriakidou / Carol V Robinson / Norimichi Nomura / So Iwata / Michael Landreh / Laura Orellana / ...Authors: Rei Matsuoka / Roman Fudim / Sukkyeong Jung / Chenou Zhang / Andre Bazzone / Yurie Chatzikyriakidou / Carol V Robinson / Norimichi Nomura / So Iwata / Michael Landreh / Laura Orellana / Oliver Beckstein / David Drew /
Abstract: The Na/H exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na/Li exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the ...The Na/H exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na/Li exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the functional importance of NHA2, structural information and the molecular basis for its ion-exchange mechanism have been lacking. Here we report the cryo-EM structures of bison NHA2 in detergent and in nanodiscs, at 3.0 and 3.5 Å resolution, respectively. The bison NHA2 structure, together with solid-state membrane-based electrophysiology, establishes the molecular basis for electroneutral ion exchange. NHA2 consists of 14 transmembrane (TM) segments, rather than the 13 TMs previously observed in mammalian Na/H exchangers (NHEs) and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. We propose that the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2
Authors: Matsuoka R / Fudim F / Jung S / Drew F
History
DepositionJul 1, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7p1k
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13163.png

Downloads & links

-
Map

FileDownload / File: emd_13163.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.01475 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.028
Minimum - Maximum-0.19577232 - 0.27119884
Average (Standard dev.)6.527174e-05 (±0.005272714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 259.776 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.014751.014751.01475
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z259.776259.776259.776
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1960.2710.000

-
Supplemental data

-
Mask #1

Fileemd_13163_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13163_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13163_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : detergent structure

EntireName: detergent structure
Components
  • Complex: detergent structure
    • Protein or peptide: mitochondrial sodium/hydrogen exchanger 9B2
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Phosphatidylinositol

-
Supramolecule #1: detergent structure

SupramoleculeName: detergent structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bison bison (American bison)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightExperimental: 57373 kDa/nm

-
Macromolecule #1: mitochondrial sodium/hydrogen exchanger 9B2

MacromoleculeName: mitochondrial sodium/hydrogen exchanger 9B2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bison bison (American bison)
Molecular weightTheoretical: 57.419203 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MRNQDKRAAH KDSEPSTEVN HTASSYQGRQ QETGMNLRGI DGNEPTEGSN LLNNNEKMQG TPAEPNHLQR RRQIHACPPR GLLARVITN VTMVILLWAV VWSVTGSECL PGGNLFGIIM LFYCAIIGGK LFGLIKLPTL PPLPPLLGML LAGFLIRNVP V ISDNIQIK ...String:
MRNQDKRAAH KDSEPSTEVN HTASSYQGRQ QETGMNLRGI DGNEPTEGSN LLNNNEKMQG TPAEPNHLQR RRQIHACPPR GLLARVITN VTMVILLWAV VWSVTGSECL PGGNLFGIIM LFYCAIIGGK LFGLIKLPTL PPLPPLLGML LAGFLIRNVP V ISDNIQIK HKWSSALRSI ALSVILVRAG LGLDSNALKK LKGVCVRLSL GPCLIEACTS AVLAYFLMGL PWQWGFMLGF VL GAVSPAV VVPSMLLLQE GGYGVEKGIP TLLMAAGSFD DILAITGFNT CLGMAFSTGS TVFNVLKGVL EVIIGVVTGL VLG FFIQYF PSSDQDNLVW KRAFLVLGLS VLAVFSSTYF GFPGSGGLCT LVTAFLAGRG WASTKTDVEK VIAVAWDIFQ PLLF GLIGA EVLITALRPE TIGLCVATLG IAVLIRILVT YLMVCFAGFN IKEKIFISFA WLPKATVQAA IGSVALDTAR SHGEK QLEG YGMDVLTVAF LSIIITAPVG SLLIGLLGPR LLQKAEQNKD EEDQGETSIQ V

-
Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #3: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 3 / Number of copies: 4 / Formula: T7X
Molecular weightTheoretical: 887.128 Da
Chemical component information

ChemComp-T7X:
Phosphatidylinositol / Phosphatidylinositol

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloridesodium chloride
50.0 mMTris-HClTrisTris hydroxy chloride
0.001 %LMNGLauryl Maltose Neopentyl Glycol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.13)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4cz9

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 362655

+
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