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 1.3 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
  • Structures With Same Primary Citation

  • 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 b ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
68 heavy chain Fab
E
212Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
68 light chain Fab
F
214Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-v
A
965Homo sapiensMutation(s): 0 
Gene Names: ITGAVMSK8VNRAVTNR
Find proteins for P06756 (Homo sapiens)
Go to UniProtKB:  P06756
NIH Common Fund Data Resources
PHAROS  P06756

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-8
B
639Homo sapiensMutation(s): 0 
Gene Names: ITGB8
Find proteins for P26012 (Homo sapiens)
Go to UniProtKB:  P26012
NIH Common Fund Data Resources
PHAROS  P26012

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
8B8 heavy chain Fab
C
213Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
8B8 light chain Fab
D
213Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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 

  • 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