9CKV

Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin

• PDB DOI: https://doi.org/10.2210/pdb9CKV/pdb
• EM Map EMD-45655: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-09 Released: 2024-07-17 
• Deposition Author(s): Werther, R., Nguyen, A., Estrada Alamo, K.A., Wang, X., Campbell, M.G.
• Funding Organization(s): The Pew Charitable Trusts, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

De Novo Design of Integrin alpha5beta1 Modulating Proteins for Regenerative Medicine

Wang, X., Guillem-Marti, J., Kumar, S., Lee, D.S., Cabrerizo-Aguado, D., Werther, R., Estrada Alamo, K.A., Zhao, Y.T., Nguyen, A., Kopyeva, I., Huang, B., Li, J., Hao, Y., Li, X., Brizuela-Velasco, A., Murray, A.N., Gerben, S., Roy, A., DeForest, C.A., Springer, T., Ruohola-Baker, H., Cooper, J.A., Campbell, M.G., Maria Manero, J., Ginebra, M., Baker, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 206.84 kDa 
• Atom Count: 6,893 
• Modelled Residue Count: 872 
• Deposited Residue Count: 1,840 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-5	A	1,005	Homo sapiens	Mutation(s): 0  Gene Names: ITGA5, FNRA
UniProt & NIH Common Fund Data Resources
Find proteins for P08648 (Homo sapiens) Explore P08648  Go to UniProtKB:  P08648
PHAROS:  P08648 GTEx:  ENSG00000161638
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P08648-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-1	B	738	Homo sapiens	Mutation(s): 0  Gene Names: ITGB1, FNRB, MDF2, MSK12
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens) Explore P05556  Go to UniProtKB:  P05556
PHAROS:  P05556 GTEx:  ENSG00000150093
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P05556-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NeoNectin	C	97	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, H, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-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	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	N [auth B], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN	P [auth B], Q [auth B], R [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	J [auth A], K [auth A], L [auth A], M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Werther, R., Nguyen, A., Estrada Alamo, K.A., Wang, X., Campbell, M.G.

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Funding Organization	Location	Grant Number
The Pew Charitable Trusts	United States	NA
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM147414-01
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30 CA015704-40; RRID:SCR_022611
Other private		Seattle Cancer Consortium Safeway Inc Pilot Grant

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release