3M1N: Human Sonic Hedgehog N-terminal domain

Crystal structure of Human Sonic Hedgehog N-terminal domain. Determined by X-ray diffraction at 1.85 Å resolution. Released 16 Mar 2010.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,971
Mol. weight: 40.43 kDa
Ligands: ZN
Released: 16 Mar 2010

Explore 3M1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M1N contains 14 α-helices and 18 β-strands across 2 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	36-43	8
β-strand	47-48	2	1
α-helix	73-75	3
β-strand	77-78	2	2
β-strand	84-86	3	1
α-helix	94-96	3
β-strand	97-98	2	2
α-helix	100-116	17
β-strand	122-126	5	1
β-strand	133	1	3
β-strand	135	1	3
α-helix	139-142	4
β-strand	145-150	6	1
α-helix	155-157	3
α-helix	158-167	10
β-strand	172-177	6	1
β-strand	180-184	5	1

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	36-43	8
β-strand	47-48	2	4
α-helix	71-75	5
β-strand	77-78	2	5
β-strand	84-86	3	4
α-helix	94-96	3
β-strand	97-98	2	5
α-helix	100-116	17
β-strand	122-126	5	4
α-helix	139-142	4
β-strand	145-150	6	4
α-helix	155-157	3
α-helix	158-167	10
β-strand	172-177	6	4
β-strand	180-184	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sonic hedgehog protein	A, B	protein	175	Homo sapiens	Q15465 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3M1N_1 Sonic hedgehog protein (chains A, B)
IIGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNP
DIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYE
GRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Mapping sonic hedgehog-receptor interactions by steric interference. Pepinsky, R.B., Rayhorn, P., Day, E.S. et al. J Biol Chem (2000) 275:10995-11001. DOI 10.1074/jbc.275.15.10995 · PubMed

Other PDB entries of the same protein (UniProt Q15465 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PJV 1.43 Å, Structure of Human Sonic Hedgehog in complex with Zinc and Magnesium
8Z3A 1.75 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 without metals
8Z39 1.8 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant L-T56A with metals
3MXW 1.83 Å, Crystal structure Sonic hedgehog bound to the 5E1 fab fragment
8Z2V 1.89 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A with…
8YYZ 1.9 Å, Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant H-R102A in the…
7URF 2.8 Å, Human HHAT H379C in complex with SHH N-terminal peptide
3HO5 3.01 Å, Crystal structure of Hedgehog-interacting protein (HHIP) and Sonic hedgehog (SHH) complex
7MHZ 3.2 Å, Human Hedgehog acyltransferase (HHAT) in complex with a palmitoylated Hedgehog peptide…
6RMG 3.4 Å, Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II
6E1H 3.5 Å, Structure of 2:1 human Ptch1-Shh-N complex
6RVD 3.5 Å, Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex

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