6DJP

Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-EM structure of the alpha v beta 8 integrin reveals a mechanism for stabilizing integrin extension.

Cormier, A.Campbell, M.G.Ito, S.Wu, S.Lou, J.Marks, J.Baron, J.L.Nishimura, S.L.Cheng, Y.

(2018) Nat Struct Mol Biol 25: 698-704

  • DOI: 10.1038/s41594-018-0093-x
  • Primary Citation of Related Structures:  
    6DJP

  • PubMed Abstract: 
  • Integrins are conformationally flexible cell surface receptors that survey the extracellular environment for their cognate ligands. Interactions with ligands are thought to be linked to global structural rearrangements involving transitions between bent, extended-closed and extended-open forms ...

    Integrins are conformationally flexible cell surface receptors that survey the extracellular environment for their cognate ligands. Interactions with ligands are thought to be linked to global structural rearrangements involving transitions between bent, extended-closed and extended-open forms. Thus far, structural details are lacking for integrins in the extended conformations due to extensive flexibility between the headpiece and legs in this conformation. Here we present single-particle electron cryomicroscopy structures of human αvβ8 integrin in the extended-closed conformation, which has been considered to be a low-affinity intermediate. Our structures show the headpiece rotating about a flexible αv knee, suggesting a ligand surveillance mechanism for integrins in their extended-closed form. Our model predicts that the extended conformation is mainly stabilized by an interface formed between flexible loops in the upper and lower domains of the αv leg. Confirming these findings with the αvβ3 integrin suggests that our model of stabilizing the extended-closed conformation is generalizable to other integrins.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA. yifan.cheng@ucsf.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin alpha-vA965Homo sapiensMutation(s): 0 
Gene Names: ITGAVMSK8VNRAVTNR
Find proteins for P06756 (Homo sapiens)
Explore P06756 
Go to UniProtKB:  P06756
NIH Common Fund Data Resources
PHAROS:  P06756
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-8B639Homo sapiensMutation(s): 0 
Gene Names: ITGB8
Find proteins for P26012 (Homo sapiens)
Explore P26012 
Go to UniProtKB:  P26012
NIH Common Fund Data Resources
PHAROS:  P26012
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
8B8 heavy chain FabC213Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
8B8 light chain FabD213Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
68 heavy chain FabE212Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
68 light chain FabF214Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG, H, J, K, L, M2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 8
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-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-glucopyranoseI6 N-Glycosylation Oligosaccharides Interaction
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseN3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
O [auth A], P [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54HL119893
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01HL113032
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01HL134183
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098672
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD020054
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41CA196276

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary