3D1M: Sonic Hedgehog

Crystal Structure of Sonic Hedgehog Bound to the third FNIII domain of CDO. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 Sept 2008.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 4,327
Mol. weight: 61.67 kDa
Ligands: ZN, CA
Released: 23 Sept 2008

Explore 3D1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D1M contains 19 α-helices and 32 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	48-49	2	1
α-helix	73-76	4
β-strand	78-79	2	2
β-strand	85-87	3	1
α-helix	95-97	3
β-strand	98-99	2	2
α-helix	101-117	17
β-strand	123-127	5	1
α-helix	136	1
α-helix	140-143	4
β-strand	146-151	6	1
α-helix	156-158	3
α-helix	159-168	10
β-strand	173-178	6	1
β-strand	181-185	5	1

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	48-49	2	3
α-helix	73-76	4
β-strand	78-79	2	4
β-strand	85-87	3	3
α-helix	95-97	3
β-strand	98-99	2	4
α-helix	101-117	17
β-strand	123-127	5	3
α-helix	136	1
α-helix	140-143	4
β-strand	146-151	6	3
α-helix	156-158	3
α-helix	159-168	10
β-strand	173-178	6	3
β-strand	181-185	5	3

Chain C: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	831-837	7	5
β-strand	843-848	6	5
β-strand	861-868	8	6
β-strand	878-883	6	6
β-strand	888-891	4	5
α-helix	894-895	2
β-strand	899-908	10	6
β-strand	911-912	2	6
β-strand	919-922	4	6

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	831-837	7	7
β-strand	843-848	6	7
α-helix	851-854	4
β-strand	861-868	8	8
α-helix	874-876	3
β-strand	878-883	6	8
β-strand	888-891	4	7
α-helix	894-895	2
β-strand	899-907	9	8
β-strand	912	1	8
β-strand	919-922	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sonic hedgehog protein	A, B	protein	168	Mus musculus	Q62226 (AlphaFold model)
Cell adhesion molecule	C, D	protein	102	Homo sapiens	Q4KMG0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3D1M_1 Sonic hedgehog protein (chains A, B)
GPGSGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKITRNSERFKELTPNY
NPDIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLH
YEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAE

Sequence of entity 2 (C, D), FASTA

>3D1M_2 Cell adhesion molecule (chains C, D)
GSTPITGPHIAYTEAVSDTQIMLKWTYIPSSNNNTPIQGFYIYYRPTDSDNDSDYKRDVV
EGSKQWHMIGHLQPETSYDIKMQCFNEGGESEFSNVMICETK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	4

Primary citation

The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla. McLellan, J.S., Zheng, X., Hauk, G. et al. Nature (2008) 455:979-983. DOI 10.1038/nature07358 · PubMed

Other PDB entries of the same protein (UniProt Q62226 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1VHH 1.7 Å, A potential catalytic site within the amino-terminal signalling domain of sonic hedgehog
4C4M 1.74 Å, Crystal structure of the Sonic Hedgehog-chondroitin-4-sulphate complex
3N1R 2.13 Å, Crystal Structure of ShhN
4C4N 2.36 Å, Crystal structure of the Sonic Hedgehog-heparin complex
7RPK 2.7 Å, Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog
2WG4 3.15 Å, Crystal structure of the complex between human hedgehog-interacting protein HIP and…
2WFX 3.2 Å, Crystal structure of the complex between human hedgehog-interacting protein HIP and…

Browse structure collections

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