Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 67.34 kDa 
• Atom Count: 4354 
• Residue Count: 559 
• Unique protein chains: 2

1XDT

COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR

• DOI: 10.2210/pdb1XDT/pdb

• Classification: COMPLEX (TOXIN/GROWTH FACTOR)
• Organism(s): Corynebacterium diphtheriae, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1997-11-18 Released: 1998-02-25 
• Deposition Author(s): Louie, G.V., Yang, W., Bowman, M.E., Choe, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.290 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 

Literature

Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor.

Louie, G.V., Yang, W., Bowman, M.E., Choe, S.

(1997) Mol Cell 1: 67-78

• PubMed: 9659904 
• DOI: 10.1016/s1097-2765(00)80008-8
• Structures With Same Primary Citation


• PubMed Abstract: 
  

We describe the crystal structure at 2.65 A resolution of diphtheria toxin (DT) complexed 1:1 with a fragment of its cell-surface receptor, the precursor of heparin-binding epidermal-growth-factor-like growth factor (HBEGF). HBEGF in the complex has the typical EGF-like fold and packs its principal beta hairpin against the face of a beta sheet in the receptor-binding domain of DT. The interface has a predominantly hydrophobic core, and polar interactions are formed at the periphery. The structure of the complex suggests that part of the membrane anchor of the receptor can interact with a hinge region of DT. The toxin molecule is thereby induced to form an open conformation conducive to membrane insertion. The structure provides a basis for altering the binding specificity of the toxin, and may also serve as a model for other EGF-receptor interactions.

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Organizational Affiliation: 

Structural Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DIPHTHERIA TOXIN	T	535	Corynebacterium diphtheriae	Mutation(s): 0  EC: 2.4.2.36
Find proteins for P00588 (Corynephage beta) Explore P00588  Go to UniProtKB:  P00588

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HEPARIN-BINDING EPIDERMAL GROWTH FACTOR	R	79	Homo sapiens	Mutation(s): 0  Gene Names: HBEGF, DTR, DTS, HEGFL
Find proteins for Q99075 (Homo sapiens) Explore Q99075  Go to UniProtKB:  Q99075
NIH Common Fund Data Resources
PHAROS  Q99075 GTEx  ENSG00000113070

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.290 
• R-Value Work: 0.172 
• R-Value Observed: 0.172 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.4	α = 90
b = 103.7	β = 90
c = 127.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-11-18 
• Released Date: 1998-02-25 
Deposition Author(s): Louie, G.V., Yang, W., Bowman, M.E., Choe, S.

Revision History 

• Version 1.0: 1998-02-25
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance