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 21MW | pdb_000021mw

Human NHA1 in an inward-open conformation

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-12-19 Released: 2026-09-30 
  • Deposition Author(s): Tang, B., Dang, S.
  • Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Cryo-EM structure of human Na + /H + exchanger NHA1 in an inward-open conformation.

Tang, B., Qiu, Q., Dang, S.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77811-7
  • Primary Citation Related Structures: 
    21MW

  • PubMed Abstract: 

    The human Na + /H + exchanger NHA1 (SLC9B1) plays a critical role in sperm motility and male fertility by regulating intracellular pH through its sodium-proton antiport activity. Despite its physiological importance, the structural and mechanistic basis of NHA1 function has remained elusive. Here, we present the cryo-EM structure of human NHA1 at 3.6 Å resolution, captured in an inward-open conformation. Structural comparisons with modeled outward-open states reveal substantial conformational changes in the core domain, supporting an elevator-like transport mechanism. Additionally, several key residues are identified that modify their interaction patterns, likely aiding in the conformational switches necessary for substrate transport. Their contribution to substrate transport is further supported by mutagenesis and sodium transport assays, providing insights into the molecular mechanism of NHA1.

    • Organizational Affiliation: 
    • Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China.

Macromolecule Content 

  • Total Structure Weight: 112.2 kDa 
  • Atom Count: 6,575 
  • Modeled Residue Count: 870 
  • Deposited Residue Count: 1,030 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium/hydrogen exchanger 9B1
A, B
515Homo sapiensMutation(s): 0 
Gene Names: SLC9B1, NHA1, NHEDC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q4ZJI4 (Homo sapiens)
Explore Q4ZJI4 
Go to UniProtKB:  Q4ZJI4
PHAROS:  Q4ZJI4
GTEx:  ENSG00000164037 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4ZJI4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF16103321
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF16102822
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF16100223
The University Grants Committee, Research Grants Council (RGC)Hong KongC6001-21E
The University Grants Committee, Research Grants Council (RGC)Hong KongC6012-22G

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release
  • Version 1.1: 2026-10-28
    Changes: Data collection, Database references