PDBsum entry 1es7

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protein Protein-protein interface(s) links
Cytokine PDB id
Jmol PyMol
Protein chains
104 a.a. *
83 a.a. *
Waters ×82
* Residue conservation analysis
PDB id:
Name: Cytokine
Title: Complex between bmp-2 and two bmp receptor ia ectodomains
Structure: Bone morphogenetic protein-2. Chain: a, c. Synonym: bmp-2. Engineered: yes. Bone morphogenetic protein receptor ia. Chain: b, d. Fragment: extracellular domain. Synonym: alk-3. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.90Å     R-factor:   0.191     R-free:   0.229
Authors: T.Kirsch,W.Sebald,M.K.Dreyer
Key ref:
T.Kirsch et al. (2000). Crystal structure of the BMP-2-BRIA ectodomain complex. Nat Struct Biol, 7, 492-496. PubMed id: 10881198 DOI: 10.1038/75903
07-Apr-00     Release date:   07-Oct-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P12643  (BMP2_HUMAN) -  Bone morphogenetic protein 2
396 a.a.
104 a.a.
Protein chains
Pfam   ArchSchema ?
P36894  (BMR1A_HUMAN) -  Bone morphogenetic protein receptor type-1A
532 a.a.
83 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains B, D: E.C.  - Receptor protein serine/threonine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + [receptor-protein] = ADP + [receptor-protein] phosphate
+ [receptor-protein]
+ [receptor-protein] phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     transmembrane receptor protein serine/threonine kinase signaling pathway   1 term 
  Biochemical function     growth factor activity     4 terms  


    Added reference    
DOI no: 10.1038/75903 Nat Struct Biol 7:492-496 (2000)
PubMed id: 10881198  
Crystal structure of the BMP-2-BRIA ectodomain complex.
T.Kirsch, W.Sebald, M.K.Dreyer.
Bone morphogenetic proteins (BMPs) belong to the large transforming growth factor-beta (TGF-beta) superfamily of multifunctional cytokines. BMP-2 can induce ectopic bone and cartilage formation in adult vertebrates and is involved in central steps in early embryonal development in animals. Signaling by these cytokines requires binding of two types of transmembrane serine/threonine receptor kinase chains classified as type I and type II. Here we report the crystal structure of human dimeric BMP-2 in complex with two high affinity BMP receptor IA extracellular domains (BRIAec). The receptor chains bind to the 'wrist' epitopes of the BMP-2 dimer and contact both BMP-2 monomers. No contacts exist between the receptor domains. The model reveals the structural basis for discrimination between type I and type II receptors and the variability of receptor-ligand interactions that is seen in BMP-TGF-beta systems.
  Selected figure(s)  
Figure 1.
Figure 1. The structure of the BMP-2 -BRIA[ec] complex. a, Side view with the membrane proximal side on the bottom and b, top view approximately along the twofold axis of the complex in a ribbon representation. The BMP monomers are colored gold and blue, the two BRIA[ec] molecules are green. Secondary structure elements, chain termini and receptor loops 1 and 3 are labeled. The 'wrist' and the putative 'knuckle' epitopes on BMP-2 are highlighted. c, Stereo view of BRIA[ec] (green) superimposed with mActRII[ec] (blue). The view is onto the palm side of the hand-like structure, which provides the binding epitope for BMP-2. Disulfide bridges are depicted in yellow and magenta for BRIA[ec] and mActRII[ec], respectively, with the same numbering as in Fig. 2. The side chain of Phe 85 in helix 1 of BRIA[ec] is shown.
Figure 4.
Figure 4. Stereo view of the hydrophobic pocket around BRIA[ec] residue Phe 85. Receptor residues Phe 85 -Cys 87 are depicted in green, BMP-2[A] residues Asn 59 -Val 63 in blue, and BMP-2[B] residues Trp 28 -Ile 32, Met 89 -Leu 92, and Tyr 103 -Met 106 in gold. The 2F[o] - F[c] electron density map was calculated omitting receptor helix residues 80 -87 and is contoured at 1.0 .
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 492-496) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21029048 C.C.Mandal, S.Ganapathy, Y.Gorin, K.Mahadev, K.Block, H.E.Abboud, S.E.Harris, G.Ghosh-Choudhury, and N.Ghosh-Choudhury (2010).
Reactive oxygen species derived from Nox4 mediate BMP2 gene transcription and osteoblast differentiation.
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20545624 C.C.Rider, and B.Mulloy (2010).
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20674464 J.W.Lowery, and Caestecker (2010).
BMP signaling in vascular development and disease.
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Bone morphogenetic protein receptors and signal transduction.
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20629020 L.Calvanese, D.Marasco, N.Doti, A.Saporito, G.D'Auria, L.Paolillo, M.Ruvo, and L.Falcigno (2010).
Structural investigations on the Nodal-Cripto binding: A theoretical and experimental approach.
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20501893 N.Ricard, M.Bidart, C.Mallet, G.Lesca, S.Giraud, R.Prudent, J.J.Feige, and S.Bailly (2010).
Functional analysis of the BMP9 response of ALK1 mutants from HHT2 patients: a diagnostic tool for novel ACVRL1 mutations.
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A selection fit mechanism in BMP receptor IA as a possible source for BMP ligand-receptor promiscuity.
  PLoS One, 5, 0.
PDB code: 3nh7
20704570 T.Liu, and X.H.Feng (2010).
Regulation of TGF-beta signalling by protein phosphatases.
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The pro-form of BMP-2 interferes with BMP-2 signalling by competing with BMP-2 for IA receptor binding.
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19229295 A.Kotzsch, J.Nickel, A.Seher, W.Sebald, and T.D.Müller (2009).
Crystal structure analysis reveals a spring-loaded latch as molecular mechanism for GDF-5-type I receptor specificity.
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PDB code: 3evs
19549280 I.Tesseur, H.Zhang, W.Brecht, J.Corn, J.S.Gong, K.Yanagisawa, M.Michikawa, K.Weisgraber, Y.Huang, and T.Wyss-Coray (2009).
Bioactive TGF-beta can associate with lipoproteins and is enriched in those containing apolipoprotein E3.
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The structure of myostatin:follistatin 288: insights into receptor utilization and heparin binding.
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PDB code: 3hh2
19926516 J.Nickel, W.Sebald, J.C.Groppe, and T.D.Mueller (2009).
Intricacies of BMP receptor assembly.
  Cytokine Growth Factor Rev, 20, 367-377.  
19345406 J.Y.Lee, J.E.Choo, Y.S.Choi, J.S.Suh, S.J.Lee, C.P.Chung, and Y.J.Park (2009).
Osteoblastic differentiation of human bone marrow stromal cells in self-assembled BMP-2 receptor-binding peptide-amphiphiles.
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19735544 K.Heinecke, A.Seher, W.Schmitz, T.D.Mueller, W.Sebald, and J.Nickel (2009).
Receptor oligomerization and beyond: a case study in bone morphogenetic proteins.
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18485004 A.Galat, G.Gross, P.Drevet, A.Sato, and A.Ménez (2008).
Conserved structural determinants in three-fingered protein domains.
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18243111 J.Groppe, C.S.Hinck, P.Samavarchi-Tehrani, C.Zubieta, J.P.Schuermann, A.B.Taylor, P.M.Schwarz, J.L.Wrana, and A.P.Hinck (2008).
Cooperative assembly of TGF-beta superfamily signaling complexes is mediated by two disparate mechanisms and distinct modes of receptor binding.
  Mol Cell, 29, 157-168.
PDB code: 2pjy
18243107 J.Massagué (2008).
A very private TGF-beta receptor embrace.
  Mol Cell, 29, 149-150.  
18200552 J.Y.Lee, J.E.Choo, H.J.Park, J.B.Park, S.C.Lee, S.J.Lee, Y.J.Park, and C.P.Chung (2008).
Synthetic peptide-coated bone mineral for enhanced osteoblastic activation in vitro and in vivo.
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Crystallization and preliminary X-ray analysis of the complex of the first von Willebrand type C domain bound to bone morphogenetic protein 2.
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18768470 R.Stamler, H.T.Keutmann, Y.Sidis, C.Kattamuri, A.Schneyer, and T.B.Thompson (2008).
  J Biol Chem, 283, 32831-32838.
PDB code: 3b4v
18056265 R.V.Korupolu, U.Muenster, J.D.Read, W.Vale, and W.H.Fischer (2008).
Activin A/bone morphogenetic protein (BMP) chimeras exhibit BMP-like activity and antagonize activin and myostatin.
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  18704304 Z.Duan, Q.Zheng, X.Guo, C.Li, B.Wu, and W.Wu (2008).
Repair of rabbit femoral defects with a novel BMP2-derived oligopeptide P24.
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17295905 D.Weber, A.Kotzsch, J.Nickel, S.Harth, A.Seher, U.Mueller, W.Sebald, and T.D.Mueller (2007).
A silent H-bond can be mutationally activated for high-affinity interaction of BMP-2 and activin type IIB receptor.
  BMC Struct Biol, 7, 6.
PDB codes: 2h62 2h64
17483092 J.L.Zhang, Y.Huang, L.Y.Qiu, J.Nickel, and W.Sebald (2007).
von Willebrand factor type C domain-containing proteins regulate bone morphogenetic protein signaling through different recognition mechanisms.
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17158104 P.M.Smallwood, J.Williams, Q.Xu, D.J.Leahy, and J.Nathans (2007).
Mutational analysis of Norrin-Frizzled4 recognition.
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17643432 P.T.Loverde, A.Osman, and A.Hinck (2007).
Schistosoma mansoni: TGF-beta signaling pathways.
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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.
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17409095 T.F.Lerch, S.Shimasaki, T.K.Woodruff, and T.S.Jardetzky (2007).
Structural and biophysical coupling of heparin and activin binding to follistatin isoform functions.
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PDB code: 2p6a
17146441 T.Shimanuki, T.Hara, T.Furuya, T.Imamura, and K.Miyazono (2007).
Modulation of the functional binding sites for TGF-beta on the type II receptor leads to suppression of TGF-beta signaling.
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16482217 A.E.Harrington, S.A.Morris-Triggs, B.T.Ruotolo, C.V.Robinson, S.Ohnuma, and M.Hyvönen (2006).
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PDB codes: 2arp 2arv
16550532 A.Saito, Y.Suzuki, M.Kitamura, S.Ogata, Y.Yoshihara, S.Masuda, C.Ohtsuki, and M.Tanihara (2006).
Repair of 20-mm long rabbit radial bone defects using BMP-derived peptide combined with an alpha-tricalcium phosphate scaffold.
  J Biomed Mater Res A, 77, 700-706.  
16606344 C.Sieber, F.Plöger, R.Schwappacher, R.Bechtold, M.Hanke, S.Kawai, Y.Muraki, M.Katsuura, M.Kimura, M.M.Rechtman, Y.I.Henis, J.Pohl, and P.Knaus (2006).
Monomeric and dimeric GDF-5 show equal type I receptor binding and oligomerization capability and have the same biological activity.
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16672363 G.P.Allendorph, W.W.Vale, and S.Choe (2006).
Structure of the ternary signaling complex of a TGF-beta superfamily member.
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PDB code: 2goo
16635802 J.F.Tobin, and A.J.Celeste (2006).
Bone morphogenetic proteins and growth differentiation factors as drug targets in cardiovascular and metabolic disease.
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16765900 X.Wang, R.H.Baloh, J.Milbrandt, and K.C.Garcia (2006).
Structure of artemin complexed with its receptor GFRalpha3: convergent recognition of glial cell line-derived neurotrophic factors.
  Structure, 14, 1083-1092.
PDB codes: 2gh0 2gyr 2gyz
15844167 B.Moussian, J.Söding, H.Schwarz, and C.Nüsslein-Volhard (2005).
Retroactive, a membrane-anchored extracellular protein related to vertebrate snake neurotoxin-like proteins, is required for cuticle organization in the larva of Drosophila melanogaster.
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15695507 F.Hillger, G.Herr, R.Rudolph, and E.Schwarz (2005).
Biophysical comparison of BMP-2, ProBMP-2, and the free pro-peptide reveals stabilization of the pro-peptide by the mature growth factor.
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16480449 G.Valdimarsdottir, and C.Mummery (2005).
Functions of the TGFbeta superfamily in human embryonic stem cells.
  APMIS, 113, 773-789.  
15948132 H.H.Keah, and M.T.Hearn (2005).
A molecular recognition paradigm: promiscuity associated with the ligand-receptor interactions of the activin members of the TGF-beta superfamily.
  J Mol Recognit, 18, 385-403.  
15744518 J.Wendler, L.F.Vallejo, U.Rinas, and U.Bilitewski (2005).
Application of an SPR-based receptor assay for the determination of biologically active recombinant bone morphogenetic protein-2.
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15851468 M.A.Brown, Q.Zhao, K.A.Baker, C.Naik, C.Chen, L.Pukac, M.Singh, T.Tsareva, Y.Parice, A.Mahoney, V.Roschke, I.Sanyal, and S.Choe (2005).
Crystal structure of BMP-9 and functional interactions with pro-region and receptors.
  J Biol Chem, 280, 25111-25118.
PDB code: 1zkz
15861141 P.Llinas, M.H.Le Du, H.Gårdsvoll, K.Danø, M.Ploug, B.Gilquin, E.A.Stura, and A.Ménez (2005).
Crystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide.
  EMBO J, 24, 1655-1663.
PDB code: 1ywh
16186117 R.W.Cook, T.B.Thompson, S.P.Kurup, T.S.Jardetzky, and T.K.Woodruff (2005).
Structural basis for a functional antagonist in the transforming growth factor beta superfamily.
  J Biol Chem, 280, 40177-40186.  
16129674 U.Muenster, C.A.Harrison, C.Donaldson, W.Vale, and W.H.Fischer (2005).
An activin-A/C chimera exhibits activin and myostatin antagonistic properties.
  J Biol Chem, 280, 36626-36632.  
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.  
15123686 C.A.Harrison, P.C.Gray, W.H.Fischer, C.Donaldson, S.Choe, and W.Vale (2004).
An activin mutant with disrupted ALK4 binding blocks signaling via type II receptors.
  J Biol Chem, 279, 28036-28044.  
14996829 E.del Re, J.L.Babitt, A.Pirani, A.L.Schneyer, and H.Y.Lin (2004).
In the absence of type III receptor, the transforming growth factor (TGF)-beta type II-B receptor requires the type I receptor to bind TGF-beta2.
  J Biol Chem, 279, 22765-22772.  
14627550 J.P.Hanrahan, S.M.Gregan, P.Mulsant, M.Mullen, G.H.Davis, R.Powell, and S.M.Galloway (2004).
Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both increased ovulation rate and sterility in Cambridge and Belclare sheep (Ovis aries).
  Biol Reprod, 70, 900-909.  
15569154 M.Sammar, S.Stricker, G.C.Schwabe, C.Sieber, A.Hartung, M.Hanke, I.Oishi, J.Pohl, Y.Minami, W.Sebald, S.Mundlos, and P.Knaus (2004).
Modulation of GDF5/BRI-b signalling through interaction with the tyrosine kinase receptor Ror2.
  Genes Cells, 9, 1227-1238.  
14746809 Caestecker (2004).
The transforming growth factor-beta superfamily of receptors.
  Cytokine Growth Factor Rev, 15, 1.  
14741627 P.Q.Ruhé, H.C.Kroese-Deutman, J.G.Wolke, P.H.Spauwen, and J.A.Jansen (2004).
Bone inductive properties of rhBMP-2 loaded porous calcium phosphate cement implants in cranial defects in rabbits.
  Biomaterials, 25, 2123-2132.  
15473835 S.J.Lee (2004).
Regulation of muscle mass by myostatin.
  Annu Rev Cell Dev Biol, 20, 61-86.  
15064755 S.Keller, J.Nickel, J.L.Zhang, W.Sebald, and T.D.Mueller (2004).
Molecular recognition of BMP-2 and BMP receptor IA.
  Nat Struct Mol Biol, 11, 481-488.
PDB codes: 1reu 1rew
15044950 V.M.Leppänen, M.M.Bespalov, P.Runeberg-Roos, U.Puurand, A.Merits, M.Saarma, and A.Goldman (2004).
The structure of GFRalpha1 domain 3 reveals new insights into GDNF binding and RET activation.
  EMBO J, 23, 1452-1462.
PDB code: 1q8d
15449706 W.Sebald, J.Nickel, J.L.Zhang, and T.D.Mueller (2004).
Molecular recognition in bone morphogenetic protein (BMP)/receptor interaction.
  Biol Chem, 385, 697-710.  
15838109 W.Vale, E.Wiater, P.Gray, C.Harrison, L.Bilezikjian, and S.Choe (2004).
Activins and inhibins and their signaling.
  Ann N Y Acad Sci, 1038, 142-147.  
12665502 C.A.Harrison, P.C.Gray, S.C.Koerber, W.Fischer, and W.Vale (2003).
Identification of a functional binding site for activin on the type I receptor ALK4.
  J Biol Chem, 278, 21129-21135.  
14633986 D.G.Winkler, M.K.Sutherland, J.C.Geoghegan, C.Yu, T.Hayes, J.E.Skonier, D.Shpektor, M.Jonas, B.R.Kovacevich, K.Staehling-Hampton, M.Appleby, M.E.Brunkow, and J.A.Latham (2003).
Osteocyte control of bone formation via sclerostin, a novel BMP antagonist.
  EMBO J, 22, 6267-6276.  
  12600237 F.Pohl, S.Hassel, A.Nohe, M.Flentje, P.Knaus, W.Sebald, and O.Koelbl (2003).
Radiation-induced suppression of the Bmp2 signal transduction pathway in the pluripotent mesenchymal cell line C2C12: an in vitro model for prevention of heterotopic ossification by radiotherapy.
  Radiat Res, 159, 345-350.  
12667445 J.Greenwald, J.Groppe, P.Gray, E.Wiater, W.Kwiatkowski, W.Vale, and S.Choe (2003).
The BMP7/ActRII extracellular domain complex provides new insights into the cooperative nature of receptor assembly.
  Mol Cell, 11, 605-617.
PDB codes: 1lx5 1lxi
12660162 T.B.Thompson, T.K.Woodruff, and T.S.Jardetzky (2003).
Structures of an ActRIIB:activin A complex reveal a novel binding mode for TGF-beta ligand:receptor interactions.
  EMBO J, 22, 1555-1566.
PDB codes: 1nys 1nyu
12912996 T.Takada, T.Katagiri, M.Ifuku, N.Morimura, M.Kobayashi, K.Hasegawa, A.Ogamo, and R.Kamijo (2003).
Sulfated polysaccharides enhance the biological activities of bone morphogenetic proteins.
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14559178 W.Sebald, and T.D.Mueller (2003).
The interaction of BMP-7 and ActRII implicates a new mode of receptor assembly.
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12809600 Y.Shi, and J.Massagué (2003).
Mechanisms of TGF-beta signaling from cell membrane to the nucleus.
  Cell, 113, 685-700.  
12154125 B.Y.Qin, S.S.Lam, J.J.Correia, and K.Lin (2002).
Smad3 allostery links TGF-beta receptor kinase activation to transcriptional control.
  Genes Dev, 16, 1950-1963.
PDB codes: 1mjs 1mk2
12121646 C.C.Boesen, S.Radaev, S.A.Motyka, A.Patamawenu, and P.D.Sun (2002).
The 1.1 A crystal structure of human TGF-beta type II receptor ligand binding domain.
  Structure, 10, 913-919.
PDB code: 1m9z
12221089 E.V.Bocharov, D.M.Korzhnev, M.J.Blommers, T.Arvinte, V.Y.Orekhov, M.Billeter, and A.S.Arseniev (2002).
Dynamics-modulated biological activity of transforming growth factor beta3.
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12478285 J.Groppe, J.Greenwald, E.Wiater, J.Rodriguez-Leon, A.N.Economides, W.Kwiatkowski, M.Affolter, W.W.Vale, J.C.Belmonte, and S.Choe (2002).
Structural basis of BMP signalling inhibition by the cystine knot protein Noggin.
  Nature, 420, 636-642.
PDB code: 1m4u
12478270 J.L.Wrana (2002).
Structural biology: On the wings of inhibition.
  Nature, 420, 613-614.  
12485160 K.Miyazawa, M.Shinozaki, T.Hara, T.Furuya, and K.Miyazono (2002).
Two major Smad pathways in TGF-beta superfamily signalling.
  Genes Cells, 7, 1191-1204.  
11850637 P.J.Hart, S.Deep, A.B.Taylor, Z.Shu, C.S.Hinck, and A.P.Hinck (2002).
Crystal structure of the human TbetaR2 ectodomain--TGF-beta3 complex.
  Nat Struct Biol, 9, 203-208.
PDB code: 1ktz
12185845 S.Souchelnytskyi, A.Moustakas, and C.H.Heldin (2002).
TGF-beta signaling from a three-dimensional perspective: insight into selection of partners.
  Trends Cell Biol, 12, 304-307.  
11880645 T.K.Bera, R.Maitra, C.Iavarone, G.Salvatore, V.Kumar, J.J.Vincent, B.K.Sathyanarayana, P.Duray, B.K.Lee, and I.Pastan (2002).
PATE, a gene expressed in prostate cancer, normal prostate, and testis, identified by a functional genomic approach.
  Proc Natl Acad Sci U S A, 99, 3058-3063.  
12297049 T.P.Garrett, N.M.McKern, M.Lou, T.C.Elleman, T.E.Adams, G.O.Lovrecz, H.J.Zhu, F.Walker, M.J.Frenkel, P.A.Hoyne, R.N.Jorissen, E.C.Nice, A.W.Burgess, and C.W.Ward (2002).
Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor alpha.
  Cell, 110, 763-773.
PDB code: 1mox
11544249 F.Docagne, N.Colloc'h, V.Bougueret, M.Page, J.Paput, M.Tripier, P.Dutartre, E.T.MacKenzie, A.Buisson, S.Komesli, and D.Vivien (2001).
A soluble transforming growth factor-beta (TGF-beta ) type I receptor mimics TGF-beta responses.
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11344456 H.Uludag, B.Norrie, N.Kousinioris, and T.Gao (2001).
Engineering temperature-sensitive poly(N-isopropylacrylamide) polymers as carriers of therapeutic proteins.
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Structural determinants of binding and specificity in transforming growth factor-receptor interactions.
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Germline mutations in BMPR1A/ALK3 cause a subset of cases of juvenile polyposis syndrome and of Cowden and Bannayan-Riley-Ruvalcaba syndromes.
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TGFbeta signaling in growth control, cancer, and heritable disorders.
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BMP-2 antagonists emerge from alterations in the low-affinity binding epitope for receptor BMPR-II.
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