9RH6 | pdb_00009rh6

Cryo-EM structure of the inward-facing apo NhaA in the plugged state at pH 6.3

PDB DOI: https://doi.org/10.2210/pdb9RH6/pdb
EM Map EMD-53959: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli, Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-08 Released: 2026-06-17
Deposition Author(s): Weng, T.-H., Safarian, S., Michel, H.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Conformational ensemble reveals pH-dependent activation and substrate recognition of the Na+/H+ antiporter NhaA

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.

To be published.

Macromolecule Content

Total Structure Weight: 70.71 kDa
Atom Count: 4,632
Modeled Residue Count: 611
Deposited Residue Count: 653
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)/H(+) antiporter NhaA	A	407	Escherichia coli	Mutation(s): 0 Gene Names: nhaA, ant, b0019, JW0018
UniProt
Find proteins for P13738 (Escherichia coli (strain K12)) Explore P13738 Go to UniProtKB: P13738
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13738
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fv6F9 heavy chain	B	127	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fv6F9 light chain	C	119	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2026-06-17
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.