6E1H: 2:1 human Ptch1-Shh-N complex

Structure of 2:1 human Ptch1-Shh-N complex. Determined by electron microscopy at 3.5 Å resolution. Released 29 Aug 2018.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 16,667
Mol. weight: 341.42 kDa
Ligands: ZN, CA, PLM
Released: 29 Aug 2018

Explore 6E1H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E1H contains 100 α-helices and 47 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: 46 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	77-95	19
α-helix	97-99	3
α-helix	102-116	15
α-helix	125-127	3
α-helix	135-145	11
β-strand	153-154	2	1
β-strand	157-162	6	2
α-helix	172-186	15
β-strand	190	1	3
β-strand	197	1	3
β-strand	203	1	1
α-helix	216-223	8
β-strand	229	1	2
α-helix	253-254	2
α-helix	261-270	10
α-helix	276-282	7
α-helix	316-317	2
β-strand	328	1	4
β-strand	336	1	4
β-strand	343-344	2	2
β-strand	359-363	5	2
β-strand	366-367	2	1
α-helix	369-375	7
α-helix	389-410	22
β-strand	417-422	6	2
α-helix	424-435	12
α-helix	439-456	18
α-helix	470-490	21
α-helix	498-501	4
α-helix	503-524	22
α-helix	536-562	27
α-helix	568-601	34
α-helix	733-740	8
α-helix	742-744	3
α-helix	747-769	23
β-strand	773	1	5
α-helix	777-780	4
α-helix	786-796	11
β-strand	800-807	8	6
α-helix	817-824	8
β-strand	832	1	6
β-strand	835	1	7
β-strand	839	1	7
α-helix	844-865	22
α-helix	878-888	11
β-strand	889	1	8
β-strand	896	1	8
α-helix	898-900	3
α-helix	919-929	11
α-helix	931-937	7
α-helix	944-946	3
α-helix	964-969	6
β-strand	972-979	8	6
α-helix	986-1004	19
β-strand	1008-1011	4	6
α-helix	1013-1018	6
α-helix	1020-1022	3
α-helix	1024-1047	24
α-helix	1050-1074	25
β-strand	1078	1	5
α-helix	1080-1092	13
α-helix	1094-1103	10
α-helix	1113-1121	9
α-helix	1124-1137	14
α-helix	1138-1140	3
α-helix	1146-1147	2
α-helix	1148-1154	7
α-helix	1155-1173	19

Chain B: 48 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	77-94	18
α-helix	101-113	13
α-helix	114-117	4
α-helix	125-129	5
α-helix	136-145	10
β-strand	157-162	6	12
α-helix	172-186	15
β-strand	203	1	13
α-helix	214-221	8
β-strand	229	1	12
α-helix	261-270	10
α-helix	276-284	9
α-helix	315	1
α-helix	317	1
α-helix	319-322	4
α-helix	339-342	4
β-strand	343-344	2	12
β-strand	359-363	5	12
β-strand	366	1	13
α-helix	367-368	2
α-helix	369-375	7
β-strand	379	1	9
α-helix	383-385	3
α-helix	389-408	20
β-strand	417-422	6	12
α-helix	425-435	11
α-helix	439-456	18
α-helix	471-490	20
α-helix	493-496	4
α-helix	497-527	31
α-helix	538-560	23
α-helix	568-605	38
α-helix	733-743	11
α-helix	747-769	23
α-helix	777-779	3
α-helix	786-796	11
β-strand	800-807	8	14
α-helix	812-814	3
α-helix	816-825	10
β-strand	835	1	15
β-strand	839	1	15
α-helix	844-863	20
α-helix	878-887	10
β-strand	889	1	16
β-strand	896	1	16
β-strand	908	1	17
β-strand	914	1	17
α-helix	916-918	3
α-helix	919-929	11
α-helix	931-936	6
α-helix	944-946	3
α-helix	962-969	8
β-strand	972-979	8	14
α-helix	986-1003	18
β-strand	1008-1012	5	14
α-helix	1014-1017	4
α-helix	1020-1046	27
α-helix	1050-1074	25
α-helix	1080-1103	24
α-helix	1112-1120	9
α-helix	1123-1140	18
α-helix	1146-1148	3
α-helix	1149-1153	5
α-helix	1154-1168	15
α-helix	1171-1174	4

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	33-37	5
α-helix	40-43	4
β-strand	44	1	9
α-helix	71-75	5
β-strand	77	1	10
β-strand	84-86	3	11
β-strand	98	1	10
α-helix	100-116	17
β-strand	122-124	3	11
α-helix	140-142	3
β-strand	146-150	5	11
α-helix	158-168	11
β-strand	172-174	3	11
β-strand	181-184	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1	A, B	protein	1447	Homo sapiens	Q13635 (AlphaFold model)
Sonic hedgehog protein	C	protein	174	Homo sapiens	Q15465 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6E1H_1 Protein patched homolog 1 (chains A, B)
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

>6E1H_2 Sonic hedgehog protein (chains C)
CGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPD
IIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEG
RAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
CA	Calcium ion	Ca	2
PLM	Palmitic acid	C16 H32 O2	1

Primary citation

Two Patched molecules engage distinct sites on Hedgehog yielding a signaling-competent complex. Qi, X., Schmiege, P., Coutavas, E. et al. Science (2018) 362. DOI 10.1126/science.aas8843 · 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
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
6OEV 3.8 Å, Structure of human Patched1 in complex with native Sonic Hedgehog
6DMB 3.9 Å, Cryo-EM structure of human Ptch1

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