1TGJ

HUMAN TRANSFORMING GROWTH FACTOR-BETA 3, CRYSTALLIZED FROM DIOXANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of TGF-beta 3 and comparison to TGF-beta 2: implications for receptor binding.

Mittl, P.R.Priestle, J.P.Cox, D.A.McMaster, G.Cerletti, N.Grutter, M.G.

(1996) Protein Sci. 5: 1261-1271

  • DOI: 10.1002/pro.5560050705
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transforming growth factors beta belong to a group of cytokines that control cellular proliferation and differentiation. Five isoforms are known that share approximately 75% sequence identity, but exert different biological activities. The structure ...

    Transforming growth factors beta belong to a group of cytokines that control cellular proliferation and differentiation. Five isoforms are known that share approximately 75% sequence identity, but exert different biological activities. The structure of TGF-beta 3 was solved by X-ray crystallography and refined to a final R-factor of 17.5% at 2.0 A resolution. Comparison with the structure of TGF-beta 2 (Schlunegger MP, Grütter MG, 1992, Nature 358:430-434; Daopin S, Piez KA, Ogawa Y, Davies DR, 1992, Science 257:369-373) reveals a virtually identical central core. Differences exist in the conformations of the N-terminal alpha-helix and in the beta-sheet loops. In TGF-beta 3, the N-terminal alpha-helix has moved approximately 1 A away from the central core. This movement can be correlated with the mutation of Leu 17 to Val and Ala 47 to Pro in TGF-beta 3. The beta-sheet loops rotate as a rigid body 9 degrees around an axis that runs approximately parallel to the dimer axis. If these differences are recognized by the TGF-beta receptors, they might account for the individual cellular responses. A molecule of the precipitating agent dioxane is bound in a crystal contact, forming a hydrogen bond with Trp 32. This dioxane may occupy a carbohydrate-binding site, because dioxane possesses some structural similarity with a carbohydrate. The dioxane is in contact with two tryptophans, which are often involved in carbohydrate recognition.


    Related Citations: 
    • Refined Crystal Structure of Human Transforming Growth Factor Beta 2 at 1.95 A Resolution
      Schlunegger, M.P.,Grutter, M.G.
      (1993) J.Mol.Biol. 231: 445


    Organizational Affiliation

    Ciba-Geigy Ltd., Pharmaceutical Research, CH-4002 Basle, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSFORMING GROWTH FACTOR-BETA 3
A
112Homo sapiensMutation(s): 0 
Gene Names: TGFB3
Find proteins for P10600 (Homo sapiens)
Go to Gene View: TGFB3
Go to UniProtKB:  P10600
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DIO
Query on DIO

Download SDF File 
Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.175 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 49.300α = 90.00
b = 49.300β = 90.00
c = 78.900γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
Agrovatadata reduction
X-PLORmodel building
MADNESdata collection
MADNESdata reduction
ROTAVATAdata reduction
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-18
    Type: Data collection, Other, Refinement description