[English] 日本語
Yorodumi
- EMDB-53968: Cryo-EM structure of the inward-facing sodium-bound NhaA at pH 8.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53968
TitleCryo-EM structure of the inward-facing sodium-bound NhaA at pH 8.5
Map data
Sample
  • Complex: NhaA in complex with Fv6F9
    • Complex: NhaA
      • Protein or peptide: Na(+)/H(+) antiporter NhaA
    • Complex: Fv6F9
      • Protein or peptide: Fv6F9 heavy chain
      • Protein or peptide: Fv6F9 light chain
  • Ligand: SODIUM ION
  • Ligand: water
KeywordsNhaA / sodium proton exchanger / TRANSPORT PROTEIN
Function / homology
Function and homology information


response to alkaline pH / sodium:proton antiporter activity / cardiolipin binding / response to salt stress / regulation of intracellular pH / plasma membrane
Similarity search - Function
Na+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1
Similarity search - Domain/homology
Na(+)/H(+) antiporter NhaA
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWeng T-H / Safarian S / Michel H
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Conformational ensemble reveals pH-dependent activation and substrate recognition of the Na+/H+ antiporter NhaA
Authors: Weng T-H / Fabian B / Olkhova E / Welsch S / Schmidt SL / Danieli T / Keren Y / Abraham R / Safarian S / Hummer G / Padan E / Michel H
History
DepositionJun 8, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53968.png

Downloads & links

-
Map

FileDownload / File: emd_53968.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 248 pix.
= 207.576 Å		0.84 Å/pix.
x 248 pix.
= 207.576 Å		0.84 Å/pix.
x 248 pix.
= 207.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0115
Minimum - Maximum-0.03399177 - 0.075938046
Average (Standard dev.)0.00006965146 (±0.001827551)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions248248248
Spacing248248248
CellA=B=C: 207.576 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_53968_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53968_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NhaA in complex with Fv6F9

EntireName: NhaA in complex with Fv6F9
Components
  • Complex: NhaA in complex with Fv6F9
    • Complex: NhaA
      • Protein or peptide: Na(+)/H(+) antiporter NhaA
    • Complex: Fv6F9
      • Protein or peptide: Fv6F9 heavy chain
      • Protein or peptide: Fv6F9 light chain
  • Ligand: SODIUM ION
  • Ligand: water

-
Supramolecule #1: NhaA in complex with Fv6F9

SupramoleculeName: NhaA in complex with Fv6F9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27 KDa

-
Supramolecule #2: NhaA

SupramoleculeName: NhaA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #3: Fv6F9

SupramoleculeName: Fv6F9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Na(+)/H(+) antiporter NhaA

MacromoleculeName: Na(+)/H(+) antiporter NhaA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.585867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPA LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI ...String:
MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPA LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI IIIALFYTND LSMASLGVAA VAIAVLAVLN LCGARRTGVY ILVGVVLWTA VLKSGVHATL AGVIVGFFIP LK EKHGRSP AKRLEHVLHP WVAYLILPLF AFANAGVSLQ GVTLDGLTSI LPLGIIAGLL IGKPLGISLF CWLALRLKLA HLP EGTTYQ QIMVVGILCG IGFTMSIFIA SLAFGSVDPE LINWAKLGIL VGSISSAVIG YSWLRVRLRP SVAAAIEGRI EGRL EHHHH HH

UniProtKB: Na(+)/H(+) antiporter NhaA

-
Macromolecule #2: Fv6F9 heavy chain

MacromoleculeName: Fv6F9 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.934411 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVKLHQSGAE LVRPGASVKL SCKALGYTFS DYEMHWVKQT PVHGLEWIGA IHPGSGGTAY NQKFKGKATL TADKSSSTAY MELSSLTSE DPAVYYCTKE EYGNDFDYWG QGTTVTVSSA WRHPQFGG

-
Macromolecule #3: Fv6F9 light chain

MacromoleculeName: Fv6F9 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.193555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DIELTQTPSS LSASLGERVS LTCRASQEIS GYLSWLQQKP DGTIKRLIYA ASTLDSGVPK RFSGSRSGSD YSLTISSLES EDFADYYCL QYASYPFTFG SGTKLEIKRE QKLISEEDLN

-
Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: RELION (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 173768
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

9rh1


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9rhf:
Cryo-EM structure of the inward-facing sodium-bound NhaA at pH 8.5

+
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