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PDBsum entry 4neh

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protein ligands metals Protein-protein interface(s) links
Cell adhesion PDB id
4neh
Jmol PyMol
Contents
Protein chains
1084 a.a.
668 a.a.
Ligands
NAG-NAG ×4
NAG-NAG-BMA
NAG-NAG-BMA-MAN-
MAN-MAN-MAN
NAG
Metals
_NA
_CA ×5
_MG ×2
_CL
Waters ×308
PDB id:
4neh
Name: Cell adhesion
Title: An internal ligand-bound, metastable state of a leukocyte in axb2
Structure: Integrin alpha-x. Chain: a. Fragment: cd11c. Synonym: cd11 antigen-like family member c, leu m5, leukocy adhesion glycoprotein p150,95 alpha chain, leukocyte adhesi receptor p150,95. Engineered: yes. Mutation: yes. Integrin beta-2.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: itgax, cd11c. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek-293. Gene: itgb2, cd18, mfi7.
Resolution:
2.75Å     R-factor:   0.194     R-free:   0.225
Authors: M.Sen,K.Yuki,T.A.Springer
Key ref: M.Sen et al. (2013). An internal ligand-bound, metastable state of a leukocyte integrin, αXβ2. J Cell Biol, 203, 629-642. PubMed id: 24385486 DOI: 10.1083/jcb.201308083
Date:
29-Oct-13     Release date:   15-Jan-14    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20702  (ITAX_HUMAN) -  Integrin alpha-X
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1163 a.a.
1084 a.a.*
Protein chain
Pfam   ArchSchema ?
P05107  (ITB2_HUMAN) -  Integrin beta-2
Seq:
Struc:
 
Seq:
Struc:
769 a.a.
668 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     tertiary granule membrane   13 terms 
  Biological process     cell adhesion   32 terms 
  Biochemical function     protein binding     10 terms  

 

 
DOI no: 10.1083/jcb.201308083 J Cell Biol 203:629-642 (2013)
PubMed id: 24385486  
 
 
An internal ligand-bound, metastable state of a leukocyte integrin, αXβ2.
M.Sen, K.Yuki, T.A.Springer.
 
  ABSTRACT  
 
How is massive conformational change in integrins achieved on a rapid timescale? We report crystal structures of a metastable, putative transition state of integrin αXβ2. The αXβ2 ectodomain is bent; however, a lattice contact stabilizes its ligand-binding αI domain in a high affinity, open conformation. Much of the αI α7 helix unwinds, loses contact with the αI domain, and reshapes to form an internal ligand that binds to the interface between the β propeller and βI domains. Lift-off of the αI domain above this platform enables a range of extensional and rotational motions without precedent in allosteric machines. Movements of secondary structure elements in the β2 βI domain occur in an order different than in β3 integrins, showing that integrin β subunits can be specialized to assume different intermediate states between closed and open. Mutations demonstrate that the structure trapped here is metastable and can enable rapid equilibration between bent and extended-open integrin conformations and up-regulation of leukocyte adhesiveness.
 

 

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