9VXW | pdb_00009vxw

Cryo-EM structure of hAQP11 in LMNG

• PDB DOI: https://doi.org/10.2210/pdb9VXW/pdb
• EM Map EMD-65443: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Aequorea victoria
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-07-20 Released: 2025-12-31 
• Deposition Author(s): Suzuki, S., Nishikawa, K., Kamegawa, A., kozai, D., Fujiyoshi, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human AQP11 reveals a trimeric architecture with a large pore.

Suzuki, S., Kamegawa, A., Kozai, D., Nishikawa, K., Irie, K., Fujiyoshi, Y.

(2026) Sci Adv 12: eaeb5769-eaeb5769

• PubMed: 41616064 
• DOI: https://doi.org/10.1126/sciadv.aeb5769
• Primary Citation Related Structures: 
  9VXW


• PubMed Abstract: 
  

  Aquaporin-11 (AQP-11) is an endoplasmic reticulum-localized water channel essential for renal development. Its structure and the molecular basis of its transport properties remained unknown. We analyzed the human AQP11 structure under cryo-electron microscopy at 2.3 Å resolution, revealing a trimeric architecture compared with other known tetrameric AQPs and a topology comprising seven transmembrane helices (Hs), including an additional N-terminal helix (H0). The channel pore is broader and more hydrophobic than that of canonical AQPs, and features a unique structure surrounding an Asn-Pro-Cys (NPC) sequence instead of the typical Asn-Pro-Ala (NPA) motif. These features provide a structural framework through which water and other small solutes can permeate AQP11. Our findings provide a blueprint for designing specific inhibitors to investigate the physiologic functions of AQP11.

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Organizational Affiliation: 
• Advanced Research Initiative, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8501, Japan.
Joint Research Course for Advanced Biomolecular Characterization, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
Department of Biophysical chemistry School of Pharmaceutical Science, Wakayama Medical University, Wakayama 640-8156, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 60.15 kDa 
• Atom Count: 1,979 
• Modeled Residue Count: 254 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin-11,sfGFP	A	537	Homo sapiens, Aequorea victoria This entity is chimeric	Mutation(s): 0  Gene Names: AQP11, AQPX1, PSEC0027, gfp
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBQ7 (Homo sapiens) Explore Q8NBQ7  Go to UniProtKB:  Q8NBQ7
GTEx:  ENSG00000178301

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D10 (Subject of Investigation/LOI)	B [auth A]	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Suzuki, S., Nishikawa, K., Kamegawa, A., kozai, D., Fujiyoshi, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H00451

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release
  
• Version 1.1: 2026-07-15
  Changes: Data collection, Database references