6OEV: Human Patched1

Structure of human Patched1 in complex with native Sonic Hedgehog. Determined by electron microscopy at 3.8 Å resolution. Released 17 Apr 2019.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,605
Mol. weight: 181.9 kDa
Ligands: ZN, NAG
Released: 17 Apr 2019

Explore 6OEV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OEV contains 56 α-helices and 23 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: 52 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	78-95	18
α-helix	97-99	3
α-helix	101-114	14
α-helix	115-117	3
α-helix	125-128	4
α-helix	135-146	12
β-strand	153-154	2	1
β-strand	158-162	5	2
α-helix	172-186	15
β-strand	203	1	1
α-helix	215-222	8
α-helix	232-234	3
α-helix	239-241	3
α-helix	253-254	2
α-helix	261-270	10
α-helix	276-282	7
α-helix	339-342	4
β-strand	343-344	2	2
β-strand	359-362	4	2
β-strand	366-367	2	1
α-helix	368	1
α-helix	369-375	7
α-helix	380-382	3
α-helix	389-409	21
β-strand	417-421	5	2
α-helix	425-435	11
α-helix	439-456	18
α-helix	463-466	4
α-helix	470-490	21
α-helix	503-524	22
α-helix	536-563	28
α-helix	568-601	34
α-helix	733-740	8
α-helix	741-744	4
α-helix	747-769	23
β-strand	773	1	3
α-helix	786-796	11
β-strand	800-807	8	4
α-helix	812-814	3
α-helix	817-824	8
β-strand	832	1	4
α-helix	833-834	2
β-strand	835	1	5
β-strand	839	1	5
α-helix	840-842	3
α-helix	844-865	22
α-helix	878-886	9
α-helix	916-918	3
α-helix	919-929	11
α-helix	931-937	7
α-helix	944-947	4
α-helix	965-969	5
β-strand	972-979	8	4
α-helix	986-1004	19
β-strand	1008-1011	4	4
α-helix	1013-1017	5
α-helix	1019-1021	3
α-helix	1024-1047	24
α-helix	1050-1074	25
β-strand	1078	1	3
α-helix	1080-1101	22
α-helix	1102-1105	4
α-helix	1113-1121	9
α-helix	1123-1138	16
α-helix	1146-1148	3
α-helix	1149-1154	6
α-helix	1155-1174	20

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	6
α-helix	72-75	4
β-strand	77-78	2	7
β-strand	85-86	2	6
α-helix	94-96	3
β-strand	97-98	2	7
α-helix	100-116	17
β-strand	122-124	3	6
β-strand	146-150	5	6
α-helix	158-168	11
β-strand	172-174	3	6
β-strand	181-184	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1	A	protein	1447	Homo sapiens	Q13635 (AlphaFold model)
Sonic hedgehog protein	C	protein	175	Homo sapiens	Q15465 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6OEV_1 Protein patched homolog 1 (chains A)
MASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGLRRAAAPDRDYLHRPSYCDAAF
ALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLKAAN
LETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEALLQHLD
SALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAK
LQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPA
DPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHAL
QTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVL
SFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSKSQGAVGLAGVLLVALS
VAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNKRIPFEDRTGEC
LKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDL
YRREDRRLDIFCCFTSPCVSRVIQVEPQAYTDTHDNTRYSPPPPYSSHSFAHETQITMQS
TVQLRTEYDPHTHVYYTTAEPRSEISVQPVTVTQDTLSCQSPESTSSTRDLLSQFSDSSL
HCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLGLLGVSLYGTTRVRDGLDLTDI
VPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLLYDLHRSFSNVKYVMLEENKQL
PKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDDGVLAYKLLVQTGSRDKPIDIS
QLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIRPHRPEWVHDKADYMPETR
LRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICSNYTSLGLSSYPNGYPFLFWEQ
YIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMVLALMTVELFGMMGLIGIKLSA
VPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLALEHMFAPVLDGAVSTLLGVLML
AGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFGPYPEVSPANGLNRLPTPSPEP
PPSVVRFAMPPGHTHSGSDSSDSEYSSQTTVSGLSEELRHYEAQQGAGGPAHQVIVEATE
NPVFAHSTVVHPESRHHPPSNPRQQPHLDSGSLPPGRQGQQPRRDPPREGLWPPPYRPRR
DAFEISTEGHSGPSNRARWGPRGARSHNPRNPASTAMGSSVPGYCQPITTVTASASVTVA
VHPPPVPGPGRNPRGGLCPGYPETDHGLFEDPHVPFHVRCERRDSKVEVIELQDVECEER
PRGSSSN

Sequence of entity 2 (C), FASTA

>6OEV_2 Sonic hedgehog protein (chains C)
XCGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNP
DIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYE
GRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structures of human Patched and its complex with native palmitoylated sonic hedgehog. Qi, X., Schmiege, P., Coutavas, E. et al. Nature (2018) 560:128-132. DOI 10.1038/s41586-018-0308-7 · 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
9MS8 3.73 Å, PTCH1 in complex with Fab6H3
6DMB 3.9 Å, Cryo-EM structure of human Ptch1

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