PDBsum entry 1u7f

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protein Protein-protein interface(s) links
Signaling protein PDB id
Protein chains
198 a.a. *
193 a.a. *
Waters ×255
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Crystal structure of the phosphorylated smad3/smad4 heterotrimeric complex
Structure: Mothers against decapentaplegic homolog 3. Chain: a, c. Fragment: mh2 and linker domains. Synonym: smad 3, mothers against dpp homolog 3, mad3, hmad- 3, jv15-2, hsmad3. Engineered: yes. Mothers against decapentaplegic homolog 4. Chain: b. Fragment: mh2 and linker domains.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: smad3, madh3. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: smad4, madh4, dpc4.
Biol. unit: Trimer (from PQS)
2.60Å     R-factor:   0.232     R-free:   0.247
Authors: B.M.Chacko,B.Y.Qin,A.Tiwari,G.Shi,S.Lam,L.J.Hayward,M.De Caestecker,K.Lin
Key ref:
B.M.Chacko et al. (2004). Structural basis of heteromeric smad protein assembly in TGF-beta signaling. Mol Cell, 15, 813-823. PubMed id: 15350224 DOI: 10.1016/j.molcel.2004.07.016
03-Aug-04     Release date:   28-Sep-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P84022  (SMAD3_HUMAN) -  Mothers against decapentaplegic homolog 3
425 a.a.
198 a.a.
Protein chain
Pfam   ArchSchema ?
Q13485  (SMAD4_HUMAN) -  Mothers against decapentaplegic homolog 4
552 a.a.
193 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 


DOI no: 10.1016/j.molcel.2004.07.016 Mol Cell 15:813-823 (2004)
PubMed id: 15350224  
Structural basis of heteromeric smad protein assembly in TGF-beta signaling.
B.M.Chacko, B.Y.Qin, A.Tiwari, G.Shi, S.Lam, L.J.Hayward, M.De Caestecker, K.Lin.
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.
  Selected figure(s)  
Figure 2.
Figure 2. Structural Comparison between the R-Smad/Smad4 Heterotrimer and R-Smad Homotrimer(A) Left, superposition of the α carbon traces of the Smad3/Smad4 heterotrimer and the Smad2 homotrimer. The homotrimeric structure of Smad2 is in gray. The Smad3 and Smad4 subunits of the heterotrimer are in green and cyan, respectively. The boxed region shows the major conformational difference, involving helix H3 and H4, between the two structures. Right, close-up view of the helix H3/H4 region of Smad4 and the corresponding region in Smad2 is shown. Helices H5, which are in similar position in both structures, are removed in the close-up view for clarity.(B) Comparison of hydrogen bonding interactions between the R-Smad/Smad4 heterotrimeric interfaces (AB, BC, and CA interfaces) and the Smad2 homotrimeric interface. The three helix bundle regions and the phosphorylated C-terminal tails are in red. The loop-helix regions and the L3 loop/β8 pockets are in blue. The unique features in the BC and AB interfaces, which are likely the key contributors to the preferential formation of the heterotrimer, are circled.
Figure 3.
Figure 3. Asp493 of Smad4 Coordinates a Buried Electrostatic Interaction in the BC Interface(A) Close-up view of the helix 4-helix 1 interaction in the Smad2 homotrimer (left) and the BC interface of the Smad3/Smad4 heterotrimer (right). The presence of aspartic acid at position 493 of Smad4 (as opposed to Tyr406 of Smad2), coupled with the shift in helix H4, results in highly favorable electrostatic interactions between Asp493 and four surrounding arginine residues. This results in improved interface contacts over those in the Smad2 homotrimeric interface.(B) The stereoview of the 2F[o] − F[c] simulated annealed omit map of the Asp493 region of S4AF.(C) Size exclusion chromatography analysis of interaction between the wild-type S4AF or S4AF(D493A) mutant with S3LC(2P) or S2LC(2P). S4AF or S4AF(D493A) mutant was mixed equal molar ratio to the S3LC(2P) or S2LC(2P), and the mixture was loaded to the size exclusion column. The eluted fractions were run on a denaturing gel and stained with Coomassie blue. The excess, uncomplexed S4AF or S4AF(D493A) eluted as a monomer with the peak around fraction 22. Interaction between the wild-type S4AF with S2LC(2P) or S3LC(2P) is indicated by their coelution as a heteromeric complex with the peak position around fraction 15. The lack of an interaction in the case of the S4AF(D493A) mutant is indicated by the near absence of the S4AF(D493A) band in the complex fractions.(D) ITC analysis of the interaction between S4AF(D493A) and S3LC(2P). The S4AF(D493A) data are in open circles. The wild-type S4AF data are in filled squares for comparison.(E) Coimmunoprecipitation analysis of Smad2/Smad4 and Smad3/Smad4 interaction. COS-1 cells were transfected with FLAG-tagged full-length Smad2 or Smad3 with or without Myc-tagged Smad4 or Smad4(D493A), and with or without the constitutively active TGF-β type I receptor (Wieser et al., 1995). Complexes were immunoprecipitated from cell extracts with an anti-FLAG antibody and immunoblotted with either anti-FLAG or anti-Myc antibody as indicated.
  The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 15, 813-823) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21217753 I.M.van de Laar, R.A.Oldenburg, G.Pals, J.W.Roos-Hesselink, Graaf, J.M.Verhagen, Y.M.Hoedemaekers, R.Willemsen, L.A.Severijnen, H.Venselaar, G.Vriend, P.M.Pattynama, M.Collée, D.Majoor-Krakauer, D.Poldermans, I.M.Frohn-Mulder, D.Micha, J.Timmermans, Y.Hilhorst-Hofstee, S.M.Bierma-Zeinstra, P.J.Willems, J.M.Kros, E.H.Oei, B.A.Oostra, M.W.Wessels, and A.M.Bertoli-Avella (2011).
Mutations in SMAD3 cause a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis.
  Nat Genet, 43, 121-126.  
20890540 L.Li, B.P.Orner, T.Huang, A.P.Hinck, and L.L.Kiessling (2010).
Peptide ligands that use a novel binding site to target both TGF-β receptors.
  Mol Biosyst, 6, 2392-2402.  
20946979 M.Vila-Perelló, and T.W.Muir (2010).
Biological applications of protein splicing.
  Cell, 143, 191-200.  
20147459 N.BabuRajendran, P.Palasingam, K.Narasimhan, W.Sun, S.Prabhakar, R.Jauch, and P.R.Kolatkar (2010).
Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors.
  Nucleic Acids Res, 38, 3477-3488.
PDB code: 3kmp
20432467 X.Zhang, J.A.Arnott, S.Rehman, W.G.Delong, A.Sanjay, F.F.Safadi, and S.N.Popoff (2010).
Src is a major signaling component for CTGF induction by TGF-beta1 in osteoblasts.
  J Cell Physiol, 224, 691-701.  
19458083 C.Millet, M.Yamashita, M.Heller, L.R.Yu, T.D.Veenstra, and Y.E.Zhang (2009).
A negative feedback control of transforming growth factor-beta signaling by glycogen synthase kinase 3-mediated Smad3 linker phosphorylation at Ser-204.
  J Biol Chem, 284, 19808-19816.  
19557331 C.Wang, L.Chen, L.Wang, and J.Wu (2009).
Crystal structure of the MH2 domain of Drosophila Mad.
  Sci China C Life Sci, 52, 539-544.
PDB code: 3gmj
19135894 S.Dupont, A.Mamidi, M.Cordenonsi, M.Montagner, L.Zacchigna, M.Adorno, G.Martello, M.J.Stinchfield, S.Soligo, L.Morsut, M.Inui, S.Moro, N.Modena, F.Argenton, S.J.Newfeld, and S.Piccolo (2009).
FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination.
  Cell, 136, 123-135.  
19254534 S.W.Chung, F.L.Miles, R.A.Sikes, C.R.Cooper, M.C.Farach-Carson, and B.A.Ogunnaike (2009).
Quantitative modeling and analysis of the transforming growth factor beta signaling pathway.
  Biophys J, 96, 1733-1750.  
18706811 D.C.Clarke, and X.Liu (2008).
Decoding the quantitative nature of TGF-beta/Smad signaling.
  Trends Cell Biol, 18, 430-442.  
18024957 E.Cocolakis, M.Dai, L.Drevet, J.Ho, E.Haines, S.Ali, and J.J.Lebrun (2008).
Smad signaling antagonizes STAT5-mediated gene transcription and mammary epithelial cell differentiation.
  J Biol Chem, 283, 1293-1307.  
  18997322 R.Hao, L.Chen, J.W.Wu, and Z.X.Wang (2008).
Structure of Drosophila Mad MH2 domain.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 986-990.
PDB code: 3dit
16904831 K.Pardali, and A.Moustakas (2007).
Actions of TGF-beta as tumor suppressor and pro-metastatic factor in human cancer.
  Biochim Biophys Acta, 1775, 21-62.  
17785517 L.Xu, X.Yao, X.Chen, P.Lu, B.Zhang, and Y.T.Ip (2007).
Msk is required for nuclear import of TGF-{beta}/BMP-activated Smads.
  J Cell Biol, 178, 981-994.  
17428344 N.C.Rockwell, and J.C.Lagarias (2007).
Flexible mapping of homology onto structure with homolmapper.
  BMC Bioinformatics, 8, 123.  
16909115 S.Inamoto, S.Iwata, T.Inamoto, S.Nomura, T.Sasaki, Y.Urasaki, O.Hosono, H.Kawasaki, H.Tanaka, N.H.Dang, and C.Morimoto (2007).
Crk-associated substrate lymphocyte type regulates transforming growth factor-beta signaling by inhibiting Smad6 and Smad7.
  Oncogene, 26, 893-904.  
17140726 T.F.Lerch, M.Xu, T.S.Jardetzky, K.E.Mayo, I.Radhakrishnan, R.Kazer, L.D.Shea, and T.K.Woodruff (2007).
The structures that underlie normal reproductive function.
  Mol Cell Endocrinol, 267, 1-5.  
17283070 W.Chen, S.S.Lam, H.Srinath, C.A.Schiffer, W.E.Royer, and K.Lin (2007).
Competition between Ski and CREB-binding protein for binding to Smad proteins in transforming growth factor-beta signaling.
  J Biol Chem, 282, 11365-11376.  
16220545 A.Ababou, and J.E.Ladbury (2006).
Survey of the year 2004: literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 19, 79-89.  
16829514 S.Gao, and A.Laughon (2006).
Decapentaplegic-responsive silencers contain overlapping mad-binding sites.
  J Biol Chem, 281, 25781-25790.  
16990801 S.Ross, E.Cheung, T.G.Petrakis, M.Howell, W.L.Kraus, and C.S.Hill (2006).
Smads orchestrate specific histone modifications and chromatin remodeling to activate transcription.
  EMBO J, 25, 4490-4502.  
16721376 V.Muralidharan, and T.W.Muir (2006).
Protein ligation: an enabling technology for the biophysical analysis of proteins.
  Nat Methods, 3, 429-438.  
16751102 W.He, D.C.Dorn, H.Erdjument-Bromage, P.Tempst, M.A.Moore, and J.Massagué (2006).
Hematopoiesis controlled by distinct TIF1gamma and Smad4 branches of the TGFbeta pathway.
  Cell, 125, 929-941.  
15817471 A.Morén, T.Imamura, K.Miyazono, C.H.Heldin, and A.Moustakas (2005).
Degradation of the tumor suppressor Smad4 by WW and HECT domain ubiquitin ligases.
  J Biol Chem, 280, 22115-22123.  
15799969 H.B.Chen, J.G.Rud, K.Lin, and L.Xu (2005).
Nuclear targeting of transforming growth factor-beta-activated Smad complexes.
  J Biol Chem, 280, 21329-21336.  
16109720 S.Gao, J.Steffen, and A.Laughon (2005).
Dpp-responsive silencers are bound by a trimeric Mad-Medea complex.
  J Biol Chem, 280, 36158-36164.  
16212511 X.H.Feng, and R.Derynck (2005).
Specificity and versatility in tgf-beta signaling through Smads.
  Annu Rev Cell Dev Biol, 21, 659-693.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.