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- EMDB-53967: Cryo-EM structure of the inward-facing apo NhaA with flexible N-t... -

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Basic information

Entry
Database: EMDB / ID: EMD-53967
TitleCryo-EM structure of the inward-facing apo NhaA with flexible N-terminus 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
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: 3.5 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

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Structure visualization

Supplemental images

emd_53967.png

Downloads & links

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Map

FileDownload / File: emd_53967.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: 0.011
Minimum - Maximum-0.030820886 - 0.050981667
Average (Standard dev.)0.00004066489 (±0.0018229313)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_53967_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53967_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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

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Supramolecule #1: NhaA in complex with Fv6F9

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

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Supramolecule #2: NhaA

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

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Supramolecule #3: Fv6F9

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

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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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

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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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 18232
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9rh1


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

PDB-9rhe:
Cryo-EM structure of the inward-facing apo NhaA with flexible N-terminus at pH 8.5

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