8OXZ | pdb_00008oxz

Rat alpha5beta1 integrin, headpiece


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Spatial N-glycan rearrangement on alpha 5 beta 1 integrin nucleates galectin-3 oligomers to determine endocytic fate.

Shafaq-Zadah, M.Dransart, E.Hamitouche, I.Wunder, C.Chambon, V.Valades-Cruz, C.A.Leconte, L.Sarangi, N.K.Robinson, J.Bai, S.K.Regmi, R.Di Cicco, A.Hovasse, A.Bartels, R.Nilsson, U.J.Cianferani-Sanglier, S.Leffler, H.Keyes, T.E.Levy, D.Raunser, S.Roderer, D.Johannes, L.

(2025) Nat Commun 16: 9461-9461

  • DOI: https://doi.org/10.1038/s41467-025-64523-7
  • Primary Citation of Related Structures:  
    8OXZ

  • PubMed Abstract: 

    Membrane glycoproteins frequently adopt different conformations when altering between active and inactive states. Here, we discover a molecular switch that exploits dynamic spatial rearrangements of N-glycans during such conformational transitions to control protein function. For the conformationally switchable cell adhesion glycoprotein α 5 β 1 integrin, we find that only the bent-closed state arranges N-glycans to nucleate the formation of up to tetrameric oligomers of the glycan-binding protein galectin-3. We propose a structural model of how these galectin-3 oligomers are built and how they clamp the bent-closed state to select it for endocytic uptake and subsequent retrograde trafficking to the Golgi for polarized distribution in cells. Our findings reveal the dynamic regulation of the glycan landscape at the cell surface to achieve oligomerization of galectin-3. Galectin-3 oligomers are thereby identified as functional decoders of defined spatial patterns of N-glycans on specifically the bent-closed conformational state of α 5 β 1 integrin and possibly other integrin family members.


  • Organizational Affiliation
    • Chemical Biology of Cancer Unit, Institut Curie, U1339 INSERM, UMR3666 CNRS, PSL Research University, Paris, France. massiullah.shafaq-zadah@curie.fr.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin subunit alpha 5A [auth P]1,099Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A0A0G2K1E2 (Rattus norvegicus)
Explore A0A0G2K1E2 
Go to UniProtKB:  A0A0G2K1E2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0G2K1E2
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin beta-1B [auth Q]799Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P49134 (Rattus norvegicus)
Explore P49134 
Go to UniProtKB:  P49134
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49134
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P49134-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth P]
D [auth P]
E [auth P]
F [auth P]
G [auth P]
C [auth P],
D [auth P],
E [auth P],
F [auth P],
G [auth P],
H [auth Q],
I [auth Q],
J [auth Q]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.03
MODEL REFINEMENTPHENIXdev 4778

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection
  • Version 1.2: 2025-11-26
    Changes: Data collection, Database references