1TGJ | pdb_00001tgj

HUMAN TRANSFORMING GROWTH FACTOR-BETA 3, CRYSTALLIZED FROM DIOXANE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 
    0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1TGJ

This is version 2.1 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: https://doi.org/10.1002/pro.5560050705
  • Primary Citation Related Structures: 
    1TGJ, 1TGK

  • 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 12.82 kDa 
  • Atom Count: 981 
  • Modeled Residue Count: 112 
  • Deposited Residue Count: 112 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRANSFORMING GROWTH FACTOR-BETA 3112Homo sapiensMutation(s): 0 
Gene Names: HTGF-BETA3
UniProt & NIH Common Fund Data Resources
Find proteins for P10600 (Homo sapiens)
Explore P10600 
Go to UniProtKB:  P10600
PHAROS:  P10600
GTEx:  ENSG00000119699 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10600
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DIO

Query on DIO



Download:Ideal Coordinates CCD File
B [auth A]1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.3α = 90
b = 49.3β = 90
c = 78.9γ = 120
Software Package:
Software NamePurpose
MADNESdata collection
ROTAVATAdata reduction
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
CCP4data scaling
ROTAVATAdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-11
    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
  • Version 1.3: 2018-04-18
    Changes: Data collection, Other, Refinement description
  • Version 2.0: 2024-04-03
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.1: 2024-10-23
    Changes: Structure summary