9CBV | pdb_00009cbv

MicroED structure of the human MP20 protein

• PDB DOI: https://doi.org/10.2210/pdb9CBV/pdb
• EM Map EMD-45428: EMDB EMDataResource

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMDmpstruc


• Deposited: 2024-06-20 Released: 2025-05-21 
• Deposition Author(s): Nicolas, W.J., Shiriaeva, A., Martynowycz, M.W., Grey, A.C., Ruma, Y., Donaldson, P.J., Gonen, T.
• Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.50 Å
• R-Value Free: 
  0.351 (Depositor) 
• R-Value Work: 
  0.332 (Depositor) 
• R-Value Observed: 
  0.333 (Depositor) 

Starting Model: in silico

Literature

Structure of the lens MP20 mediated adhesive junction.

Nicolas, W.J., Shiriaeva, A., Martynowycz, M.W., Grey, A.C., Ruma, Y.N., Donaldson, P.J., Gonen, T.

(2025) Nat Commun 16: 2977-2977

• PubMed: 40140346 
• DOI: https://doi.org/10.1038/s41467-025-57903-6
• Primary Citation of Related Structures:  
  9CBV


• PubMed Abstract: 
  

  Human lens fiber membrane intrinsic protein MP20 is the second most abundant membrane protein of the human eye lens. Despite decades of effort its structure and function remained elusive. Here, we determined the MicroED structure of full-length human MP20 in lipidic-cubic phase to a resolution of 3.5 Å. MP20 forms tetramers each of which contain 4 transmembrane α-helices that are packed against one another forming a helical bundle. We find that each MP20 tetramer formed adhesive interactions with an opposing tetramer in a head-to-head fashion. Investigation of MP20 localization in human lenses indicate that in young fiber cells MP20 is initially localized to the cytoplasm in differentiating fiber cells but upon fiber cell maturation is inserted into the plasma membrane, correlating with the restriction of the diffusion of extracellular tracers into the lens. Together these results suggest that MP20 forms lens thin junctions in vivo, confirming its role as a structural protein in the human eye lens essential for its optical transparency.

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Organizational Affiliation: 
• Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA.
Department of Physiology, School of Medical Sciences, University of Auckland, Auckland, New Zealand.
Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA. [e-mail].
Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.16 kDa 
• Atom Count: 1,323 
• Modeled Residue Count: 166 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lens fiber membrane intrinsic protein	A	218	Homo sapiens	Mutation(s): 0  Gene Names: LIM2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P55344 (Homo sapiens) Explore P55344  Go to UniProtKB:  P55344
PHAROS:  P55344 GTEx:  ENSG00000105370

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 3.50 Å
• R-Value Free:  0.351 (Depositor) 
• R-Value Work:  0.332 (Depositor) 
• R-Value Observed: 0.333 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.18	α = 90
b = 56.18	β = 90
c = 142.5	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Nicolas, W.J., Shiriaeva, A., Martynowycz, M.W., Grey, A.C., Ruma, Y., Donaldson, P.J., Gonen, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Eye Institute (NIH/NEI)	United States	P41GM136508
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release