5FN7

Crystal structure of human CD45 extracellular region, domains d1-d2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Initiation of T Cell Signaling by Cd45 Segregation at 'Close Contacts'.

Chang, V.T.Fernandes, R.A.Ganzinger, K.A.Lee, S.F.Siebold, C.Mccoll, J.Jonsson, P.Palayret, M.Harlos, K.Coles, C.H.Jones, E.Y.Lui, Y.Huang, E.Gilbert, R.J.Klenerman, D.Aricescu, A.R.Davis, S.J.

(2016) Nat Immunol 17: 574

  • DOI: https://doi.org/10.1038/ni.3392
  • Primary Citation of Related Structures:  
    5FMV, 5FN6, 5FN7, 5FN8

  • PubMed Abstract: 

    It has been proposed that the local segregation of kinases and the tyrosine phosphatase CD45 underpins T cell antigen receptor (TCR) triggering, but how such segregation occurs and whether it can initiate signaling is unclear. Using structural and biophysical analysis, we show that the extracellular region of CD45 is rigid and extends beyond the distance spanned by TCR-ligand complexes, implying that sites of TCR-ligand engagement would sterically exclude CD45. We also show that the formation of 'close contacts', new structures characterized by spontaneous CD45 and kinase segregation at the submicron-scale, initiates signaling even when TCR ligands are absent. Our work reveals the structural basis for, and the potent signaling effects of, local CD45 and kinase segregation. TCR ligands have the potential to heighten signaling simply by holding receptors in close contacts.


  • Organizational Affiliation

    Radcliffe Department of Medicine and MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE C
A, B
186Homo sapiensMutation(s): 0 
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P08575 (Homo sapiens)
Explore P08575 
Go to UniProtKB:  P08575
PHAROS:  P08575
GTEx:  ENSG00000081237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08575
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
HG
Query on HG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.61α = 90
b = 149.61β = 90
c = 52.73γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
autoSHARPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary