5VQF

Crystal Structure of pro-TGF-beta 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 3RJR - determined by Zhu, J.H., Shi, M.L., Springer, T.A.  

Literature

Prodomain-growth factor swapping in the structure of pro-TGF-beta 1.

Zhao, B.Xu, S.Dong, X.Lu, C.Springer, T.A.

(2018) J. Biol. Chem. 293: 1579-1589

  • DOI: 10.1074/jbc.M117.809657
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transforming growth factor (TGF)-β is synthesized as a proprotein that dimerizes in the endoplasmic reticulum. After processing in the Golgi to cleave the N-terminal prodomain from the C-terminal growth factor (GF) domain in each monomer, pro-TGF-β i ...

    Transforming growth factor (TGF)-β is synthesized as a proprotein that dimerizes in the endoplasmic reticulum. After processing in the Golgi to cleave the N-terminal prodomain from the C-terminal growth factor (GF) domain in each monomer, pro-TGF-β is secreted and stored in latent complexes. It is unclear which prodomain and GF monomer are linked prior to proprotein convertase (PC) cleavage, and how much conformational change occurs following cleavage. We have determined a structure of pro-TGF-β1 with the PC cleavage site mutated, to mimic the structure of the TGF-β1 proprotein. Structure, mutation, and model building demonstrate that the prodomain arm domain in one monomer is linked to the GF that interacts with the arm domain in the other monomer in the dimeric structure, i.e., the prodomain arm domain and GF domain in each monomer are swapped. Swapping has important implications for the mechanism of biosynthesis in the TGF-β family and is relevant to the mechanism for preferential formation of heterodimers over homodimers for some members of the TGF-β family. Our structure, together with two previous ones, also provides insights into which regions of the prodomain-GF complex are highly structurally conserved, and which are perturbed by crystal lattice contacts.


    Related Citations: 
    • Latent TGF-beta structure and activation.
      Shi, M.,Zhu, J.,Wang, R.,Chen, X.,Mi, L.,Walz, T.,Springer, T.A.
      (2011) Nature 474: 343


    Organizational Affiliation

    Childrens Hospital Boston and Department of Biological Chemistry and Molecular Pharmacology Harvard, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transforming growth factor beta-1
A, B, C, D
363Sus scrofaMutation(s): 2 
Gene Names: TGFB1
Find proteins for P07200 (Sus scrofa)
Go to Gene View: TGFB1
Go to UniProtKB:  P07200
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.660α = 90.00
b = 126.920β = 96.70
c = 137.920γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata processing
PDB_EXTRACTdata extraction
SOLVEphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin DiseasesUnited StatesR01AR067288

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references, Structure summary
  • Version 1.2: 2018-02-14
    Type: Database references