7MHZ: Human Hedgehog acyltransferase

Human Hedgehog acyltransferase (HHAT) in complex with a palmitoylated Hedgehog peptide product and a Fab antibody fragment. Determined by electron microscopy at 3.2 Å resolution. Released 16 Jun 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 6,189
Mol. weight: 148.47 kDa
Ligands: PLM, HEM, PKZ, AJP
Released: 16 Jun 2021

Explore 7MHZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MHZ contains 36 α-helices and 26 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: 33 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-27	24
α-helix	33-39	7
β-strand	42-44	3	1
α-helix	51	1
β-strand	52-54	3	1
α-helix	58-66	9
α-helix	67-71	5
α-helix	72-88	17
α-helix	93-128	36
α-helix	133-148	16
α-helix	150-159	10
α-helix	164-189	26
α-helix	193-195	3
α-helix	201-208	8
α-helix	211-213	3
α-helix	217-221	5
α-helix	222-228	7
α-helix	237-264	28
α-helix	267-272	6
α-helix	274-279	6
α-helix	282-314	33
α-helix	318-324	7
α-helix	331-337	7
α-helix	340-346	7
α-helix	347-351	5
α-helix	352-354	3
α-helix	357-359	3
α-helix	360-379	20
α-helix	383-406	24
α-helix	409-418	10
α-helix	421-447	27
α-helix	450-456	7
α-helix	457-463	7
α-helix	465-469	5
α-helix	470-487	18

Chain O: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	22-25	4	2
β-strand	29-30	2	3
β-strand	36-44	9	2
α-helix	48-50	3
β-strand	53-58	6	4
β-strand	64-71	8	4
β-strand	76-79	4	4
β-strand	88-92	5	2
β-strand	99-105	7	2
α-helix	111	1
β-strand	112-118	7	4
β-strand	125-128	4	4
β-strand	132-133	2	4
β-strand	134-135	2	3

Chain P: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	5
β-strand	29-31	3	6
β-strand	38-44	7	5
β-strand	49	1	7
β-strand	55	1	7
β-strand	57-62	6	6
β-strand	69-72	4	6
β-strand	90	1	5
β-strand	94-99	6	5
β-strand	109-114	6	6
α-helix	120	1
β-strand	121	1	4
β-strand	126-129	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sonic hedgehog protein N-product peptide	B	protein	8	Homo sapiens	Q15465 (AlphaFold model)
Protein-cysteine N-palmitoyltransferase HHAT	A	protein	493	Homo sapiens	Q5VTY9 (AlphaFold model)
3H02 Fab heavy chain	O	protein	462	Mus musculus
3H02 Fab light chain	P	protein	207	Mus musculus

Sequence of entity 1 (B), FASTA

>7MHZ_1 Sonic hedgehog protein N-product peptide (chains B)
CGPGRGFG

Sequence of entity 2 (A), FASTA

>7MHZ_2 Protein-cysteine N-palmitoyltransferase HHAT (chains A)
MLPRWELALYLLASLGFHFYSFYEVYKVSREHEEELDQEFELETDTLFGGLKKDATDFEW
SFWMEWGKQWLVWLLLGHMVVSQMATLLARKHRPWILMLYGMWACWCVLGTPGVAMVLLH
TTISFCVAQFRSQLLTWLCSLLLLSTLRLQGVEEVKRRWYKTENEYYLLQFTLTVRCLYY
TSFSLELCWQQLPAASTSYSFPWMLAYVFYYPVLHNGPILSFSEFIKQMQQQEHDSLKAS
LCVLALGLGRLLCWWWLAELMAHLMYMHAIYSSIPLLETVSCWTLGGLALAQVLFFYVKY
LVLFGVPALLMRLDGLTPPALPRCVSTMFSFTGMWRYFDVGLHNFLIRYVYIPVGGSQHG
LLGTLFSTAMTFAFVSYWHGGYDYLWCWAALNWLGVTVENGVRRLVETPCIQDSLARYFS
PQARRRFHAALASCSTSMLILSNLVFLGGNEVGKTYWNRIFIQGWPWVTLSVLGFLYCYS
HVGIAWAQTYATD

Sequence of entity 3 (O), FASTA

>7MHZ_3 3H02 Fab heavy chain (chains O)
MGWSCIILFLVATATGVHSQIQLVQSGPELKKPGETVKISCKASGYTFTNYGMNWVRQAP
GKGLKWMGWINTYTGEPTYADDFKGRFAFSLETSASTAYLQINNLKDEDMATYFCARVWN
YDYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC
GCKPCICTVPEVSSVFIFPPKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWFVDDVEVH
TAQTQPREEQFNSTFRSVSELPIMHQDWLNGKEFKCRVNSAAFPAPIEKTISKTKGRPKA
PQVYTIPPPKEQMAKDKVSLTCMITDFFPEDITVEWQWNGQPAENYKNTQPIMNTNGSYF
VYSKLNVQKSNWEAGNTFTCSVLHEGLHNHHTEKSLSHSPGK

Sequence of entity 4 (P), FASTA

>7MHZ_4 3H02 Fab light chain (chains P)
MKLPVRLLVLMFWIPASRSDVLMTQTPLSLPVSLGDQVSISCRSSQSIVHSNGNTYLEWY
LQKPGQSPKLLIYRVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPW
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTK

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	1
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1
PKZ	Palmitoyl-CoA	C37 H66 N7 O17 P3 S	3
AJP	Digitonin	C56 H92 O29	10

Primary citation

Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT. Jiang, Y., Benz, T.L., Long, S.B. Science (2021) 372:1215-1219. DOI 10.1126/science.abg4998 · 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
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
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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