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- PDB-9rh1: Cryo-EM structure of the consensus inward-facing apo NhaA dimer a... -

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Basic information

Entry
Database: PDB / ID: 9rh1
TitleCryo-EM structure of the consensus inward-facing apo NhaA dimer at pH 7.5
Components
  • Fv6F9 heavy chain
  • Fv6F9 light chain
  • Na(+)/H(+) antiporter NhaA
KeywordsTRANSPORT PROTEIN / NhaA / sodium proton exchanger / cardiolipin
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
CARDIOLIPIN / Chem-PGT / Na(+)/H(+) antiporter NhaA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWeng, T.-H. / Safarian, S. / Michel, H.
Funding support Germany, 1items
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, S.L. / Danieli, T. / Keren, Y. / Abraham, R. / Safarian, S. / Hummer, G. / Padan, E. / Michel, H.
History
DepositionJun 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na(+)/H(+) antiporter NhaA
B: Fv6F9 heavy chain
C: Fv6F9 light chain
D: Na(+)/H(+) antiporter NhaA
E: Fv6F9 heavy chain
F: Fv6F9 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,6438
Polymers141,4286
Non-polymers2,2152
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Na(+)/H(+) antiporter NhaA / Na(+)/H(+) exchanger / Na(+)/Li(+)/H(+) antiporter / Sodium/proton antiporter NhaA


Mass: 43585.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nhaA, ant, b0019, JW0018 / Production host: Escherichia coli (E. coli) / References: UniProt: P13738
#2: Antibody Fv6F9 heavy chain


Mass: 13934.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Fv6F9 light chain


Mass: 13193.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#5: Chemical ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H79O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1NhaA in complex with Fv6F9COMPLEX#1-#30MULTIPLE SOURCES
2NhaACOMPLEX#11RECOMBINANT
3Fv6F9COMPLEX#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.07 MDaNO
210.043 MDaNO
310.027 MDaNO
43
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
33Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 2100 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5aparticle selection
2PHENIX1.20.1_4487model refinement
5RELION4CTF correction
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5317495
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144462 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-IDSource nameTypeDetails (eV)
14AU5

4au5

A4AU5A1PDBexperimental model
2Otherothergenerated by ModelAngelo
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039422
ELECTRON MICROSCOPYf_angle_d0.6512804
ELECTRON MICROSCOPYf_dihedral_angle_d7.6171352
ELECTRON MICROSCOPYf_chiral_restr0.0441508
ELECTRON MICROSCOPYf_plane_restr0.0051572

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