3KFD | pdb_00003kfd

Ternary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 ?
  • R-Value Free: 
    0.268 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ternary complex of transforming growth factor-beta1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily.

Radaev, S.Zou, Z.Huang, T.Lafer, E.M.Hinck, A.P.Sun, P.D.

(2010) J Biological Chem 285: 14806-14814

  • DOI: https://doi.org/10.1074/jbc.M109.079921
  • Primary Citation of Related Structures:  
    3KFD

  • PubMed Abstract: 

    Transforming growth factor (TGF)-beta1, -beta2, and -beta3 are 25-kDa homodimeric polypeptides that play crucial nonoverlapping roles in embryogenesis, tissue development, carcinogenesis, and immune regulation. Here we report the 3.0-A resolution crystal structure of the ternary complex between human TGF-beta1 and the extracellular domains of its type I and type II receptors, TbetaRI and TbetaRII. The TGF-beta1 ternary complex structure is similar to previously reported TGF-beta3 complex except with a 10 degrees rotation in TbetaRI docking orientation. Quantitative binding studies showed distinct kinetics between the receptors and the isoforms of TGF-beta. TbetaRI showed significant binding to TGF-beta2 and TGF-beta3 but not TGF-beta1, and the binding to all three isoforms of TGF-beta was enhanced considerably in the presence of TbetaRII. The preference of TGF-beta2 to TbetaRI suggests a variation in its receptor recruitment in vivo. Although TGF-beta1 and TGF-beta3 bind and assemble their ternary complexes in a similar manner, their structural differences together with differences in the affinities and kinetics of their receptor binding may underlie their unique biological activities. Structural comparisons revealed that the receptor-ligand pairing in the TGF-beta superfamily is dictated by unique insertions, deletions, and disulfide bonds rather than amino acid conservation at the interface. The binding mode of TbetaRII on TGF-beta is unique to TGF-betas, whereas that of type II receptor for bone morphogenetic protein on bone morphogenetic protein appears common to all other cytokines in the superfamily. Further, extensive hydrogen bonds and salt bridges are present at the high affinity cytokine-receptor interfaces, whereas hydrophobic interactions dominate the low affinity receptor-ligand interfaces.


  • Organizational Affiliation

    Structural Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming growth factor beta-1A,
B,
G [auth C],
H [auth D]
112Homo sapiensMutation(s): 0 
Gene Names: TGFB1TGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P01137 (Homo sapiens)
Explore P01137 
Go to UniProtKB:  P01137
PHAROS:  P01137
GTEx:  ENSG00000105329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01137
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TGF-beta receptor type-2C [auth E],
D [auth F],
I [auth G],
J [auth H]
116Homo sapiensMutation(s): 0 
Gene Names: TGFBR2
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P37173 (Homo sapiens)
Explore P37173 
Go to UniProtKB:  P37173
PHAROS:  P37173
GTEx:  ENSG00000163513 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37173
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TGF-beta receptor type-1E [auth I],
F [auth J],
K,
L
85Homo sapiensMutation(s): 0 
Gene Names: TGFBR1
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens)
Explore P36897 
Go to UniProtKB:  P36897
PHAROS:  P36897
GTEx:  ENSG00000106799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36897
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 ?
  • R-Value Free:  0.268 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 37.7¦Á = 64.01
b = 99.35¦Â = 84.47
c = 102.7¦Ă = 84.34
Software Package:
Software NamePurpose
PHASERphasing
EPMRphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary
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