1EXZ | pdb_00001exz

STRUCTURE OF STEM CELL FACTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.294 (Depositor), 0.332 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.295 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1EXZ

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human stem cell factor: implication for stem cell factor receptor dimerization and activation.

Zhang, Z.Zhang, R.Joachimiak, A.Schlessinger, J.Kong, X.P.

(2000) Proc Natl Acad Sci U S A 97: 7732-7737

  • DOI: https://doi.org/10.1073/pnas.97.14.7732
  • Primary Citation Related Structures: 
    1EXZ

  • PubMed Abstract: 

    Stem cell factor (SCF) plays important roles in hematopoiesis and the survival, proliferation, and differentiation of mast cells, melanocytes, and germ cells. SCF mediates its biological effects by binding to and activating a receptor tyrosine kinase designated c-kit or SCF receptor. In this report we describe the 2.3-A crystal structure of the functional core of recombinant human SCF. SCF is a noncovalent homodimer composed of two slightly wedged protomers. Each SCF protomer exhibits an antiparallel four-helix bundle fold. Dimerization is mediated by extensive polar and nonpolar interactions between the two protomers with a large buried surface area. Finally, we have identified a hydrophobic crevice and a charged region at the tail of each protomer that functions as a potential receptor-binding site. On the basis of these observations, a model for SCF small middle dotc-kit complex formation and dimerization is proposed.


  • Organizational Affiliation
    • Departments of Pharmacology and Biochemistry and Skirball Institute, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.

Macromolecule Content 

  • Total Structure Weight: 64.83 kDa 
  • Atom Count: 4,236 
  • Modeled Residue Count: 528 
  • Deposited Residue Count: 564 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
STEM CELL FACTOR
A, B, C, D
141Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P21583 (Homo sapiens)
Explore P21583 
Go to UniProtKB:  P21583
PHAROS:  P21583
GTEx:  ENSG00000049130 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21583
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SM

Query on SM



Download:Ideal Coordinates CCD File
F [auth B],
G [auth B],
H [auth C],
I [auth C]
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
K [auth D]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
J [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.294 (Depositor), 0.332 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.295 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.154α = 90
b = 87.526β = 97.76
c = 79.434γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary