3BN3 | pdb_00003bn3

crystal structure of ICAM-5 in complex with aL I domain


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.10 Å
  • R-Value Free:&nbsp
    0.235 (Depositor), 0.240 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.191 (Depositor), 0.200 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.193&nbsp(Depositor)&nbsp

Starting Models: experimental
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wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 2.3 of the entry. See complete&nbsphistory.&nbsp


Literature

An unusual allosteric mobility of the C-terminal helix of a high-affinity alpha L integrin I domain variant bound to ICAM-5

Zhang, H.,&nbspCasasnovas, J.M.,&nbspJin, M.,&nbspLiu, J.H.,&nbspGahmberg, C.G.,&nbspSpringer, T.A.,&nbspWang, J.-h.

(2008) Mol Cell&nbsp31: 432-437

  • DOI:&nbsphttps://doi.org/10.1016/j.molcel.2008.06.022
  • Primary Citation of Related Structures: &nbsp
    3BN3

  • PubMed Abstract:&nbsp

    Integrins are cell surface receptors that transduce signals bidirectionally across the plasma membrane. The key event of integrin signaling is the allosteric regulation between its ligand-binding site and the C-terminal helix (alpha7) of integrin's inserted (I) domain. A significant axial movement of the alpha7 helix is associated with the open, active conformation of integrins. We describe the crystal structure of an engineered high-affinity I domain from the integrin alpha(L)beta(2) (LFA-1) alpha subunit in complex with the N-terminal two domains of ICAM-5, an adhesion molecule expressed in telencephalic neurons. The finding that the alpha7 helix swings out and inserts into a neighboring I domain in an upside-down orientation in the crystals implies an intrinsically unusual mobility of this helix. This remarkable feature allows the alpha7 helix to trigger integrin's large-scale conformational changes with little energy penalty. It serves as a mechanistic example of how a weakly bound adhesion molecule works in signaling.


  • Organizational Affiliation:&nbsp

    Department of Medical Oncology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-L180Homo sapiensMutation(s): 3&nbsp
Gene Names:&nbspITGAL,&nbspCD11A
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP20701&nbsp(Homo sapiens)
Explore&nbspP20701&nbsp
Go to UniProtKB: &nbspP20701
PHAROS: &nbspP20701
GTEx: &nbspENSG00000005844&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20701
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Intercellular adhesion molecule 5196Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspICAM5,&nbspTLCN,&nbspTLN
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspQ9UMF0&nbsp(Homo sapiens)
Explore&nbspQ9UMF0&nbsp
Go to UniProtKB: &nbspQ9UMF0
PHAROS: &nbspQ9UMF0
GTEx: &nbspENSG00000105376&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMF0
Glycosylation
Glycosylation Sites: 5Go to GlyGen: Q9UMF0-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: &nbspG42666HT
GlyCosmos: &nbspG42666HT
GlyGen: &nbspG42666HT
Small Molecules
Ligands&nbsp3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File&nbsp
E [auth B],
F [auth B],
G [auth B],
H [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File&nbsp
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File&nbsp
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.10 Å
  • R-Value Free:&nbsp 0.235 (Depositor), 0.240 (DCC)&nbsp
  • R-Value Work:&nbsp 0.191 (Depositor), 0.200 (DCC)&nbsp
  • R-Value Observed:&nbsp0.193&nbsp(Depositor)&nbsp
Space Group:&nbspP 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.793α = 90
b = 71.507β = 90
c = 143.871γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-20
    Changes: Structure summary