8Z39: Sonic hedgehog

Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant L-T56A with metals. Determined by X-ray diffraction at 1.8 Å resolution. Released 16 Apr 2025.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,208
Mol. weight: 71.75 kDa
Ligands: ZN, CA
Released: 16 Apr 2025

Explore 8Z39 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Z39 contains 26 α-helices and 51 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: 7 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

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	10-12	3	4
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	34-40	7	4
β-strand	44-51	8	4
β-strand	58-60	3	4
α-helix	62-64	3
β-strand	68-73	6	3
α-helix	74-76	3
β-strand	78-83	6	3
α-helix	88-90	3
β-strand	92-98	7	4
β-strand	108-109	2	4
β-strand	113-117	5	4
α-helix	121-122	2
β-strand	123	1	5
α-helix	124-125	2
β-strand	126-130	5	6
β-strand	141-151	11	6
β-strand	152	1	5
β-strand	157-160	4	7
α-helix	161-163	3
β-strand	165	1	7
β-strand	169-171	3	6
α-helix	172-174	3
β-strand	175-176	2	6
β-strand	182-191	10	6
α-helix	192-194	3
β-strand	201-206	6	7
α-helix	207-209	3
β-strand	211-216	6	7

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	4
β-strand	19-25	7	8
β-strand	33-38	6	4
β-strand	45-49	5	4
β-strand	53-54	2	4
α-helix	55	1
β-strand	62-66	5	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	4
α-helix	96	1
β-strand	97-98	2	4
β-strand	102-107	6	4
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sonic hedgehog protein N-product	A	protein	169	Homo sapiens	Q15465 (AlphaFold model)
Heavy chain of antibody 5E1	H	protein	241	Homo sapiens
Light chain of antibody 5E1	L	protein	236	Homo sapiens

Sequence of entity 1 (A), FASTA

>8Z39_1 Sonic hedgehog protein N-product (chains A)
GFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKD
EENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDI
TTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Sequence of entity 2 (H), FASTA

>8Z39_2 Heavy chain of antibody 5E1 (chains H)
QVQLQQSGPELVRPGVSVKISCKGSGYTFIDEALHWVKQSHAESLEWIGVIRPYSGETNY
NQKFKDKATMTVDISSSTAYLELARLTSEDSAIYYCARDWERGDFFDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKEQKLISEEDLNSAVDHHHHH
H

Sequence of entity 3 (L), FASTA

>8Z39_3 Light chain of antibody 5E1 (chains L)
GDIVMTQTPKFLLVSAGDKVTITCKASQSVSNDLTWYQQKPGQSPKLLIYYASNRYAGVP
DRFTGSGYGTDFTFTISTVQAEDLAVYFCQQDYGSPPTFGGGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECEQKLISEEDLNSAVDHHHHHH

Ligands and cofactors

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

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

Primary citation

Biophysical insights to improve affinity of antibodies to fluctuated epitope of antigen: A case of anti-Shh antibody 5E1 against Shh antigen. Kaneda, I., Matsunaga, R., Nagatoishi, S. et al. To be published.

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
3MXW 1.83 Å, Crystal structure Sonic hedgehog bound to the 5E1 fab fragment
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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