7UZE | pdb_00007uze

Erythrocyte ankyrin-1 complex class 2 local refinement of AQP1 (C4 symmetry applied)

• PDB DOI: https://doi.org/10.2210/pdb7UZE/pdb
• EM Map EMD-26886: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-05-09 Released: 2022-07-20 
• Deposition Author(s): Vallese, F., Kim, K., Yen, L.Y., Johnston, J.D., Noble, A.J., Cali, T., Clarke, O.B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Architecture of the human erythrocyte ankyrin-1 complex.

Vallese, F., Kim, K., Yen, L.Y., Johnston, J.D., Noble, A.J., Cali, T., Clarke, O.B.

(2022) Nat Struct Mol Biol 29: 706-718

• PubMed: 35835865 
• DOI: https://doi.org/10.1038/s41594-022-00792-w
• Primary Citation Related Structures: 
  7UZ3, 7UZE, 7UZQ, 7UZS, 7UZU, 7UZV, 7V07, 7V0K, 7V0M, 7V0Q, 7V0S, 7V0T, 7V0U, 7V0X, 7V0Y, 7V19, 8CRQ, 8CRR, 8CRT, 8CS9, 8CSL, 8CSV, 8CSW, 8CSX, 8CSY, 8CT2, 8CT3, 8CTE


• PubMed Abstract: 
  

  The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2, glycophorin A and glycophorin B. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and, unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering.

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Organizational Affiliation: 
• Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.
Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA.
Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
Department of Biomedical Sciences, University of Padua, Padua, Italy.
Padua Neuroscience Center (PNC), University of Padua, Padua, Italy.
Study Center for Neurodegeneration (CESNE), University of Padua, Padua, Italy.
Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA. [e-mail].
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA. [e-mail].
Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 116.7 kDa 
• Atom Count: 7,577 
• Modeled Residue Count: 988 
• Deposited Residue Count: 1,076 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin-1	A [auth D], B, C, D [auth A]	269	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P29972 (Homo sapiens) Explore P29972  Go to UniProtKB:  P29972
PHAROS:  P29972 GTEx:  ENSG00000240583

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	E [auth D], F [auth B], G [auth C], H [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
P1L	A [auth D], B, C, D [auth A]	L-PEPTIDE LINKING	C19 H37 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Vallese, F., Kim, K., Yen, L.Y., Johnston, J.D., Noble, A.J., Cali, T., Clarke, O.B.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2022-07-27
  Changes: Database references
• Version 1.2: 2026-03-04
  Changes: Data collection, Refinement description, Structure summary