PDBsum entry 3d1m

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protein metals Protein-protein interface(s) links
Signaling protein / cell adhesion PDB id
Protein chains
148 a.a. *
87 a.a. *
99 a.a. *
_CA ×4
_ZN ×2
Waters ×410
* Residue conservation analysis
PDB id:
Name: Signaling protein / cell adhesion
Title: Crystal structure of sonic hedgehog bound to the third fniii cdo
Structure: Sonic hedgehog protein. Chain: a, b. Fragment: n-terminal domain, sonic hedgehog protein n-produ residues 26-189. Synonym: shh, hhg-1, sonic hedgehog protein n-product, soni protein c-product. Engineered: yes. Cell adhesion molecule. Chain: c, d.
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: shh, hhg1. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606.
1.70Å     R-factor:   0.189     R-free:   0.229
Authors: J.S.Mclellan,D.J.Leahy
Key ref:
J.S.McLellan et al. (2008). The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla. Nature, 455, 979-983. PubMed id: 18794898 DOI: 10.1038/nature07358
06-May-08     Release date:   23-Sep-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q62226  (SHH_MOUSE) -  Sonic hedgehog protein
437 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
Q4KMG0  (CDON_HUMAN) -  Cell adhesion molecule-related/down-regulated by oncogenes
1287 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
Q4KMG0  (CDON_HUMAN) -  Cell adhesion molecule-related/down-regulated by oncogenes
1287 a.a.
99 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell communication   3 terms 


DOI no: 10.1038/nature07358 Nature 455:979-983 (2008)
PubMed id: 18794898  
The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla.
J.S.McLellan, X.Zheng, G.Hauk, R.Ghirlando, P.A.Beachy, D.J.Leahy.
Hedgehog (Hh) proteins specify tissue pattern in metazoan embryos by forming gradients that emanate from discrete sites of expression and elicit concentration-dependent cellular differentiation or proliferation responses. Cellular responses to Hh and the movement of Hh through tissues are both precisely regulated, and abnormal Hh signalling has been implicated in human birth defects and cancer. Hh signalling is mediated by its amino-terminal domain (HhN), which is dually lipidated and secreted as part of a multivalent lipoprotein particle. Reception of the HhN signal is modulated by several cell-surface proteins on responding cells, including Patched (Ptc), Smoothened (Smo), Ihog (known as CDO or CDON in mammals) and the vertebrate-specific proteins Hip (also known as Hhip) and Gas1 (ref. 11). Drosophila Ihog and its vertebrate homologues CDO and BOC contain multiple immunoglobulin and fibronectin type III (FNIII) repeats, and the first FNIII repeat of Ihog binds Drosophila HhN in a heparin-dependent manner. Surprisingly, pull-down experiments suggest that a mammalian Sonic hedgehog N-terminal domain (ShhN) binds a non-orthologous FNIII repeat of CDO. Here we report biochemical, biophysical and X-ray structural studies of a complex between ShhN and the third FNIII repeat of CDO. We show that the ShhN-CDO interaction is completely unlike the HhN-Ihog interaction and requires calcium, which binds at a previously undetected site on ShhN. This site is conserved in nearly all Hh proteins and is a hotspot for mediating interactions between ShhN and CDO, Ptc, Hip and Gas1. Mutations in vertebrate Hh proteins causing holoprosencephaly and brachydactyly type A1 map to this calcium-binding site and disrupt interactions with these partners.
  Selected figure(s)  
Figure 1.
Figure 1: A calcium-binding site on Shh is important for interactions with CDOFn3. a, Sedimentation velocity results for a 1:1 mixture of 20.5 M ShhN and CDOFn3 in the absence (top) and presence (bottom) of 1 mM CaCl[2]. Solid grey lines indicate the experimental sedimentation coefficients for monomeric CDOFn3 and ShhN. The dashed line indicates the sedimentation coefficient calculated in HYDROPRO for the 1:1 complex. b, Semi-transparent molecular surface over a ribbon diagram of ShhN (yellow) bound to CDOFn3 (blue). Calcium and zinc ions are depicted as green and purple spheres, respectively. c, The ShhN–CDOFn3 interface shown in the same orientation as in b. The mostly acidic residues on CDOFn3 that interact with mostly basic residues on ShhN are labelled. Semi-transparent surface representations are shown for CDO Val 918, Met 919 and Ile 920, which make van der Waals contacts with Shh His 134 and the methylene groups of Glu 90. d, Side chains in ShhN directly coordinating the two calcium ions are shown in stick representation. Calcium ions are green and three water molecules are shown as red spheres. Hydrogen bonds are depicted as dotted lines. All structure images were rendered with PyMOL (
Figure 2.
Figure 2: Shh binds CDO differently than Hh binds Ihog. a, Schematic of Ihog and CDO. b, Ribbon diagram of the ShhN/CDOFn3 structure superimposed on the HhN/IhogFn1-2 structure by alignment of the Hh molecules. ShhN is coloured yellow, CDOFn3 dark blue, HhN red, IhogFn1 light green, and IhogFn2 light blue. Calcium and zinc ions are depicted as green and purple spheres, respectively. The boxed area shows a close-up of the interface between IhogFn1 and the Hh proteins. The side chains of four ShhN residues changed in the ShhN-Fly mutant are shown as sticks. c, ITC data for ShhN and CDOFn3 with calcium (left) and HhN and IhogFn1-2 with heparin and calcium (right). d, ITC data for ShhN and IhogFn1-2 with heparin and calcium (left) and ShhN-Fly and IhogFn1-2 with heparin and EGTA (right).
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nature (2008, 455, 979-983) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21257310 A.Gallet (2011).
Hedgehog morphogen: from secretion to reception.
  Trends Cell Biol, 21, 238-246.  
21502959 P.W.Ingham, Y.Nakano, and C.Seger (2011).
Mechanisms and functions of Hedgehog signalling across the metazoa.
  Nat Rev Genet, 12, 393-406.  
21167941 R.Ghirlando (2011).
The analysis of macromolecular interactions by sedimentation equilibrium.
  Methods, 54, 145-156.  
20024066 B.Z.Stanton, and L.F.Peng (2010).
Small-molecule modulators of the Sonic Hedgehog signaling pathway.
  Mol Biosyst, 6, 44-54.  
21044292 D.Camp, K.Currie, A.Labbé, D.J.van Meyel, and F.Charron (2010).
Ihog and Boi are essential for Hedgehog signaling in Drosophila.
  Neural Dev, 5, 28.  
20231458 E.H.Williams, W.N.Pappano, A.M.Saunders, M.S.Kim, D.J.Leahy, and P.A.Beachy (2010).
Dally-like core protein and its mammalian homologues mediate stimulatory and inhibitory effects on Hedgehog signal response.
  Proc Natl Acad Sci U S A, 107, 5869-5874.  
20536384 H.R.Maun, D.Kirchhofer, and R.A.Lazarus (2010).
Pseudo-active sites of protease domains: HGF/Met and Sonic hedgehog signaling in cancer.
  Biol Chem, 391, 881-892.  
19935712 L.Yang, G.Xie, Q.Fan, and J.Xie (2010).
Activation of the hedgehog-signaling pathway in human cancer and the clinical implications.
  Oncogene, 29, 469-481.  
20844013 P.A.Beachy, S.G.Hymowitz, R.A.Lazarus, D.J.Leahy, and C.Siebold (2010).
Interactions between Hedgehog proteins and their binding partners come into view.
  Genes Dev, 24, 2001-2012.  
20024692 S.Guo, J.Zhou, B.Gao, J.Hu, H.Wang, J.Meng, X.Zhao, G.Ma, C.Lin, Y.Xiao, W.Tang, X.Zhu, K.S.Cheah, G.Feng, D.Chan, and L.He (2010).
Missense mutations in IHH impair Indian Hedgehog signaling in C3H10T1/2 cells: Implications for brachydactyly type A1, and new targets for Hedgehog signaling.
  Cell Mol Biol Lett, 15, 153-176.  
21098113 T.R.Hartman, D.Zinshteyn, H.K.Schofield, E.Nicolas, A.Okada, and A.M.O'Reilly (2010).
Drosophila Boi limits Hedgehog levels to suppress follicle stem cell proliferation.
  J Cell Biol, 191, 943-952.  
21118524 W.R.Jackman, J.J.Yoo, and D.W.Stock (2010).
Hedgehog signaling is required at multiple stages of zebrafish tooth development.
  BMC Dev Biol, 10, 119.  
20048000 X.Zheng, R.K.Mann, N.Sever, and P.A.Beachy (2010).
Genetic and biochemical definition of the Hedgehog receptor.
  Genes Dev, 24, 57-71.  
19561611 B.Bishop, A.R.Aricescu, K.Harlos, C.A.O'Callaghan, E.Y.Jones, and C.Siebold (2009).
Structural insights into hedgehog ligand sequestration by the human hedgehog-interacting protein HHIP.
  Nat Struct Mol Biol, 16, 698-703.
PDB codes: 2wfq 2wfr 2wft 2wfx 2wg3 2wg4
19252479 B.Gao, J.Hu, S.Stricker, M.Cheung, G.Ma, K.F.Law, F.Witte, J.Briscoe, S.Mundlos, L.He, K.S.Cheah, and D.Chan (2009).
A mutation in Ihh that causes digit abnormalities alters its signalling capacity and range.
  Nature, 458, 1196-1200.  
19478089 D.C.Martinelli, and C.M.Fan (2009).
A Sonic Hedgehog Missense Mutation Associated with Holoprosencephaly Causes Defective Binding to GAS1.
  J Biol Chem, 284, 19169-19172.  
19603532 E.Roessler, K.B.El-Jaick, C.Dubourg, J.I.Vélez, B.D.Solomon, D.E.Pineda-Alvarez, F.Lacbawan, N.Zhou, M.Ouspenskaia, A.Paulussen, H.J.Smeets, U.Hehr, C.Bendavid, S.Bale, S.Odent, V.David, and M.Muenke (2009).
The mutational spectrum of holoprosencephaly-associated changes within the SHH gene in humans predicts loss-of-function through either key structural alterations of the ligand or its altered synthesis.
  Hum Mutat, 30, E921-E935.  
19561609 I.Bosanac, H.R.Maun, S.J.Scales, X.Wen, A.Lingel, J.F.Bazan, Sauvage, S.G.Hymowitz, and R.A.Lazarus (2009).
The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling.
  Nat Struct Mol Biol, 16, 691-697.
PDB codes: 3ho3 3ho4 3ho5
19840373 J.Bibliowicz, and J.M.Gross (2009).
Expanded progenitor populations, vitreo-retinal abnormalities, and Müller glial reactivity in the zebrafish leprechaun/patched2 retina.
  BMC Dev Biol, 9, 52.  
19369399 M.Cortes, A.T.Baria, and N.B.Schwartz (2009).
Sulfation of chondroitin sulfate proteoglycans is necessary for proper Indian hedgehog signaling in the developing growth plate.
  Development, 136, 1697-1706.  
19876929 V.L.Ruiz-Perez, and J.A.Goodship (2009).
Ellis-van Creveld syndrome and Weyers acrodental dysostosis are caused by cilia-mediated diminished response to hedgehog ligands.
  Am J Med Genet C Semin Med Genet, 151, 341-351.  
19040769 T.R.Bürglin (2008).
The Hedgehog protein family.
  Genome Biol, 9, 241.  
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 codes are shown on the right.