7NXD

Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation

  • Classification: CELL ADHESION
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-03-18 Released: 2021-08-25 
  • Deposition Author(s): Schumacher, S., Dedden, D., Vazquez Nunez, R., Matoba, K., Takagi, J., Biertumpfel, C., Mizuno, N.
  • Funding Organization(s): Max Planck Society, Other private, European Research Council (ERC), European Molecular Biology Organization (EMBO), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into integrin alpha 5 beta 1 opening by fibronectin ligand.

Schumacher, S.Dedden, D.Nunez, R.V.Matoba, K.Takagi, J.Biertumpfel, C.Mizuno, N.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abe9716
  • Primary Citation of Related Structures:  
    7NWL, 7NXD

  • PubMed Abstract: 

    Integrin α 5 β 1 is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and α 5 β 1 undergo conformational changes. While this is key for cell-tissue connections, its mechanism is unknown. Here, we report cryo-electron microscopy structures of native human α 5 β 1 with fibronectin to 3.1-angstrom resolution, and in its resting state to 4.6-angstrom resolution. The α 5 β 1 -fibronectin complex revealed simultaneous interactions at the arginine-glycine-aspartate loop, the synergy site, and a newly identified binding site proximal to adjacent to metal ion-dependent adhesion site, inducing the translocation of helix α1 to secure integrin opening. Resting α 5 β 1 adopts an incompletely bent conformation, challenging the model of integrin sharp bending inhibiting ligand binding. Our biochemical and structural analyses showed that affinity of α 5 β 1 for fibronectin is increased with manganese ions (Mn 2+ ) while adopting the half-bent conformation, indicating that ligand-binding affinity does not depend on conformation, and α 5 β 1 opening is induced by ligand-binding.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-51,008Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08648 (Homo sapiens)
Explore P08648 
Go to UniProtKB:  P08648
PHAROS:  P08648
GTEx:  ENSG00000161638 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08648
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-1778Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens)
Explore P05556 
Go to UniProtKB:  P05556
PHAROS:  P05556
GTEx:  ENSG00000150093 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05556
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E, M, O, P
3N/AN-Glycosylation
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
4N/AN-Glycosylation
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, I, J, K
F, H, I, J, K, L, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G
6N/AN-Glycosylation
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
V [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
Q [auth A]
R [auth A]
S [auth A]
T [auth A]
U [auth A]
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
X [auth B],
Y [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
W [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX1.17.1 Release 3660

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Other privateGermanyBoehringer Ingelheim Foundation Plus 3 Program
European Research Council (ERC)European UnionERC-CoG 724209
European Molecular Biology Organization (EMBO)European UnionYoung Investigator Program
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United States--
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release