3MXW: Crystal structure Sonic hedgehog

Crystal structure Sonic hedgehog bound to the 5E1 fab fragment. Determined by X-ray diffraction at 1.83 Å resolution. Released 26 May 2010.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,005
Mol. weight: 66.88 kDa
Ligands: ZN, CA
Released: 26 May 2010

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

Secondary structure: helices and β-sheets

3MXW contains 27 α-helices and 52 β-strands across 3 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
β-strand	47-48	2	1
α-helix	72-75	4
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
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
α-helix	188-190	3

Chain H: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	10-12	3	4
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	45-52	8	4
β-strand	56-59	4	4
α-helix	61-63	3
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-95	8	4
β-strand	100K-103	4	4
β-strand	107-111	5	4
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	131-132	2	10
β-strand	135-145	11	10
β-strand	146	1	9
α-helix	149-150	2
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	10-14	5	4
β-strand	19-25	7	3
β-strand	33-38	6	4
β-strand	45-49	5	4
β-strand	53-54	2	4
α-helix	55	1
β-strand	62-67	6	3
β-strand	70-75	6	3
α-helix	80-82	3
β-strand	84-90	7	4
β-strand	97-98	2	4
β-strand	102-107	6	4
β-strand	111	1	5
α-helix	112-113	2
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153-154	2	7
α-helix	155	1
β-strand	159-163	5	6
α-helix	164-167	4
β-strand	173-182	10	6
α-helix	183-186	4
β-strand	191-197	7	7
β-strand	205-210	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sonic hedgehog protein	A	protein	169	Homo sapiens	Q15465 (AlphaFold model)
5E1 light chain	L	protein	214	Homo sapiens
5E1 heavy chain	H	protein	220	Homo sapiens

Sequence of entity 1 (A), FASTA

>3MXW_1 Sonic hedgehog protein (chains A)
GFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKD
EENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDI
TTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Sequence of entity 2 (L), FASTA

>3MXW_2 5E1 light chain (chains L)
DIVMTQTPKFLLVSAGDKVTITCKASQSVSNDLTWYQQKPGQSPKLLIYYASNRYTGVPD
RFTGSGYGTDFTFTISTVQAEDLAVYFCQQDYGSPPTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>3MXW_3 5E1 heavy chain (chains H)
QVQLQQSGPELVRPGVSVKISCKGSGYTFIDEALHWVKQSHAESLEWIGVIRPYSGETNY
NQKFKDKATMTVDISSSTAYLELARLTSEDSAIYYCARDWERGDFFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
CA	Calcium ion	Ca	2

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

Primary citation

Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site. Maun, H.R., Wen, X., Lingel, A. et al. J Biol Chem (2010) 285:26570-26580. DOI 10.1074/jbc.M110.112284 · 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
3M1N 1.85 Å, Crystal structure of Human Sonic Hedgehog N-terminal domain
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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