9MS8: PTCH1

PTCH1 in complex with Fab6H3. Determined by electron microscopy at 3.73 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 3.73 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 9,290
Mol. weight: 145.41 kDa
Released: 2 Apr 2025

Explore 9MS8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MS8 contains 55 α-helices and 31 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: 52 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	77-95	19
α-helix	97-99	3
α-helix	100-115	16
α-helix	125-128	4
α-helix	135-145	11
β-strand	154	1	1
β-strand	158-162	5	2
α-helix	172-186	15
β-strand	203	1	1
α-helix	216-223	8
α-helix	231-234	4
α-helix	253	1
α-helix	261-270	10
α-helix	276-284	9
α-helix	339-342	4
β-strand	343-344	2	2
β-strand	359-361	3	2
β-strand	366	1	1
α-helix	367-368	2
α-helix	369-376	8
α-helix	389-410	22
β-strand	417-421	5	2
α-helix	424-435	12
α-helix	439-456	18
α-helix	470-490	21
α-helix	503-527	25
α-helix	536-562	27
α-helix	568-601	34
α-helix	734-745	12
α-helix	747-769	23
α-helix	777-779	3
α-helix	786-797	12
β-strand	800-807	8	3
α-helix	817-824	8
α-helix	825-828	4
β-strand	832	1	3
β-strand	835	1	4
β-strand	839	1	4
α-helix	840-842	3
α-helix	844-865	22
α-helix	872-874	3
α-helix	878-888	11
α-helix	898-900	3
α-helix	916-918	3
α-helix	919-929	11
α-helix	931-937	7
α-helix	945-947	3
α-helix	957-959	3
α-helix	967-969	3
β-strand	972-979	8	3
α-helix	986-1004	19
β-strand	1009	1	3
α-helix	1013-1017	5
α-helix	1020-1022	3
α-helix	1024-1047	24
α-helix	1050-1074	25
α-helix	1080-1104	25
α-helix	1113-1121	9
α-helix	1124-1138	15
α-helix	1139-1142	4
α-helix	1146-1147	2
α-helix	1148-1154	7
α-helix	1155-1165	11
α-helix	1166-1170	5
α-helix	1171-1175	5

Chain H: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	7
β-strand	36-42	7	7
β-strand	53-58	6	8
β-strand	64-70	7	8
β-strand	77-79	3	8
β-strand	87-92	6	7
β-strand	97-103	7	7
β-strand	112-114	3	8
β-strand	128	1	8

Chain L: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	5
β-strand	38-44	7	5
α-helix	50-52	3
β-strand	53-58	6	6
α-helix	63-64	2
β-strand	65-69	5	6
β-strand	82	1	5
β-strand	85-87	3	5
β-strand	90-95	6	5
α-helix	100-102	3
β-strand	105-110	6	6
β-strand	122	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1	A	protein	1094	Homo sapiens	Q13635 (AlphaFold model)
6H3 Fab light chain	L	protein	102	Mus musculus
6H3 Fab heavy chain	H	protein	110	Mus musculus

Sequence of entity 1 (A), FASTA

>9MS8_1 Protein patched homolog 1 (chains A)
MASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGLRRAAAPDRDYLHRPSYCDAAF
ALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLKAAN
LETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEALLQHLD
SALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAK
LQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPA
DPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHAL
QTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVL
SFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSKSQGAVGLAGVLLVALS
VAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNKRIPFEDRTGEC
LKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDL
YRREDRRLDIFCCFTSPCHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLGLLG
VSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLLYDL
HRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDDGVL
AYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIR
PHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICSNYT
SLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMVLAL
MTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLALEHM
FAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFGPYP
EVSPANDYKDDDDK

Sequence of entity 2 (L), FASTA

>9MS8_2 6H3 Fab light chain (chains L)
VLTQSPAIMSASLGERVTLTCTASSSVTSSYLHWYQQKPGSSPKLWIYSTSNLPFGVSPR
FSGSGSGTSFSLTISSMEAEDAATYYCHQFHRSPYTFGGGTK

Sequence of entity 3 (H), FASTA

>9MS8_3 6H3 Fab heavy chain (chains H)
EVQLVESGGGLVKPGGSRKLSCVASGFTLSDYGMHWVRQAPEKGLEWVAYIGSDSYTIYH
ADTMKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCGRNYGMDYWGQGTS

Primary citation

Inhibiting hedgehog signal by a patched-1 antibody. Hu, Q., Qi, X., Donnelly, L. et al. Cell Discov (2025) 11:29-29. DOI 10.1038/s41421-025-00772-6 · PubMed

Other PDB entries of the same protein (UniProt Q13635 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RTW 1.9 Å, Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and…
6RTX 1.95 Å, Crystal structure of the Patched-1 (PTCH1) ectodomain 1
6RTY 2.1 Å, Crystal structure of the Patched ectodomain in complex with nanobody NB64
6RVC 2.2 Å, Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75
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
6OEU 3.5 Å, Structure of human Patched1
6RVD 3.5 Å, Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex
6DMY 3.6 Å, Cryo-EM structure of human Ptch1 and ShhN complex
6N7H 3.6 Å, Cryo-EM structure of the 2:1 hPtch1-Shhp complex
6OEV 3.8 Å, Structure of human Patched1 in complex with native Sonic Hedgehog
6DMB 3.9 Å, Cryo-EM structure of human Ptch1

Browse structure collections

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