4OIB

Crystal Structure of ICAM-5 D1-D4 ectodomain fragment, Space Group R3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.273 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Crystal structures of an ICAM-5 ectodomain fragment show electrostatic-based homophilic adhesions.

Recacha, R.Jimenez, D.Tian, L.Barredo, R.Gahmberg, C.G.Casasnovas, J.M.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1934-1943

  • DOI: https://doi.org/10.1107/S1399004714009468
  • Primary Citation of Related Structures:  
    4OI9, 4OIA, 4OIB

  • PubMed Abstract: 

    Intercellular cell adhesion molecule-5 (ICAM-5) is a member of the ICAM subfamily that is exclusively expressed in the telencephalon region of the brain. The crystal structure of the four most N-terminal glycosylated domains (D1-D4) of ICAM-5 was determined in three different space groups and the D1-D5 fragment was modelled. The structures showed a curved molecule with two pronounced interdomain bends between D2 and D3 and between D3 and D4, as well as some interdomain flexibility. In contrast to ICAM-1, ICAM-5 has patches of positive and negative electrostatic charge at D1-D2 and at D3-D5, respectively. ICAM-5 can mediate homotypic interactions. In the crystals, several charge-based intermolecular interactions between the N-terminal and C-terminal moieties of the ICAM-5 molecules were observed, which defined an interacting surface in the D1-D4 fragment. One of the crystal lattices has a molecular assembly that could represent the homophilic ICAM-5 cell adhesion complex in neurons.


  • Organizational Affiliation

    Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, Darwin 3,, 28049 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intercellular adhesion molecule 5378Homo sapiensMutation(s): 0 
Gene Names: ICAM5TLCNTLN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMF0 (Homo sapiens)
Explore Q9UMF0 
Go to UniProtKB:  Q9UMF0
PHAROS:  Q9UMF0
GTEx:  ENSG00000105376 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMF0
Glycosylation
Glycosylation Sites: 9Go to GlyGen: Q9UMF0-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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-glucopyranose
D, F
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.273 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.56α = 90
b = 228.56β = 90
c = 69.98γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary