6DJP

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-v
A
965Homo sapiensMutation(s): 0 
Gene Names: ITGAV (MSK8, VNRA, VTNR)
Find proteins for P06756 (Homo sapiens)
Go to Gene View: ITGAV
Go to UniProtKB:  P06756
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-8
B
639Homo sapiensMutation(s): 0 
Gene Names: ITGB8
Find proteins for P26012 (Homo sapiens)
Go to Gene View: ITGB8
Go to UniProtKB:  P26012
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
8B8 heavy chain Fab
C
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
8B8 light chain Fab
D
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
68 heavy chain Fab
E
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
68 light chain Fab
F
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54HL119893
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01HL113032
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01HL134183
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM098672
National Institutes of Health/National Institute of General Medical SciencesUnited StatesS10OD020054
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41CA196276

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-08
    Type: Data collection, Database references
  • Version 1.2: 2018-08-15
    Type: Data collection, Database references