1U7F | pdb_00001u7f

Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex

• PDB DOI: https://doi.org/10.2210/pdb1U7F/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-08-03 Released: 2004-09-28 
• Deposition Author(s): Chacko, B.M., Qin, B.Y., Tiwari, A., Shi, G., Lam, S., Hayward, L.J., de Caestecker, M., Lin, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.247 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Structural basis of heteromeric smad protein assembly in tgf-Beta signaling

Chacko, B.M., Qin, B.Y., Tiwari, A., Shi, G., Lam, S., Hayward, L.J., De Caestecker, M., Lin, K.

(2004) Mol Cell 15: 813-823

• PubMed: 15350224 
• DOI: https://doi.org/10.1016/j.molcel.2004.07.016
• Primary Citation Related Structures: 
  1U7F, 1U7V


• PubMed Abstract: 
  

  The formation of protein complexes between phosphorylated R-Smads and Smad4 is a central event in the TGF-beta signaling pathway. We have determined the crystal structure of two R-Smad/Smad4 complexes, Smad3/Smad4 to 2.5 angstroms, and Smad2/Smad4 to 2.7 angstroms. Both complexes are heterotrimers, comprising two phosphorylated R-Smad subunits and one Smad4 subunit, a finding that was corroborated by isothermal titration calorimetry and mutational studies. Preferential formation of the R-Smad/Smad4 heterotrimer over the R-Smad homotrimer is largely enthalpy driven, contributed by the unique presence of strong electrostatic interactions within the heterotrimeric interfaces. The study supports a common mechanism of Smad protein assembly in TGF-beta superfamily signaling.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71 kDa 
• Atom Count: 4,983 
• Modeled Residue Count: 587 
• Deposited Residue Count: 635 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog 3	A, C	198	Homo sapiens	Mutation(s): 2  Gene Names: SMAD3, MADH3
UniProt & NIH Common Fund Data Resources
Find proteins for P84022 (Homo sapiens) Explore P84022  Go to UniProtKB:  P84022
PHAROS:  P84022 GTEx:  ENSG00000166949

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog 4	B	239	Homo sapiens	Mutation(s): 0  Gene Names: SMAD4, MADH4, DPC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13485 (Homo sapiens) Explore Q13485  Go to UniProtKB:  Q13485
PHAROS:  Q13485 GTEx:  ENSG00000141646

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.247 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.240 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.471	α = 90
b = 60.545	β = 90
c = 205.779	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Chacko, B.M., Qin, B.Y., Tiwari, A., Shi, G., Lam, S., Hayward, L.J., de Caestecker, M., Lin, K.

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary