1KTZ | pdb_00001ktz

Crystal Structure of the Human TGF-beta Type II Receptor Extracellular Domain in Complex with TGF-beta3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the human TbetaR2 ectodomain--TGF-beta3 complex.

Hart, P.J.Deep, S.Taylor, A.B.Shu, Z.Hinck, C.S.Hinck, A.P.

(2002) Nat Struct Biol 9: 203-208

  • DOI: https://doi.org/10.1038/nsb766
  • Primary Citation Related Structures: 
    1KTZ

  • PubMed Abstract: 

    Transforming growth factor-beta (TGF-beta) is the prototype of a large family of structurally related cytokines that play key roles in maintaining cellular homeostasis by signaling through two classes of functionally distinct Ser/Thr kinase receptors, designated as type I and type II. TGF-beta initiates receptor assembly by binding with high affinity to the type II receptor. Here, we present the 2.15 A crystal structure of the extracellular ligand-binding domain of the human TGF-beta type II receptor (ecTbetaR2) in complex with human TGF-beta3. ecTbetaR2 interacts with homodimeric TGF-beta3 by binding identical finger segments at opposite ends of the growth factor. Relative to the canonical 'closed' conformation previously observed in ligand structures across the superfamily, ecTbetaR2-bound TGF-beta3 shows an altered arrangement of its monomeric subunits, designated the 'open' conformation. The mode of TGF-beta3 binding shown by ecTbetaR2 is compatible with both ligand conformations. This, in addition to the predicted mode for TGF-beta binding to the type I receptor ectodomain (ecTbetaR1), suggests an assembly mechanism in which ecTbetaR1 and ecTbetaR2 bind at adjacent positions on the ligand surface and directly contact each other via protein--protein interactions.


  • Organizational Affiliation
    • Department of Biochemistry and Center for Biomolecular Structure Analysis, University of Texas Health Science Center at San Antonio, 78229-3900, USA.

Macromolecule Content 

  • Total Structure Weight: 26.59 kDa 
  • Atom Count: 1,656 
  • Modeled Residue Count: 188 
  • Deposited Residue Count: 234 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRANSFORMING GROWTH FACTOR BETA 3112Homo sapiensMutation(s): 0 
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TGF-beta Type II Receptor122Homo sapiensMutation(s): 0 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.30 (UniProt)
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.41α = 90
b = 114.41β = 90
c = 209.43γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary