6N7K: Tetrameric Ptch1

Cryo-EM structure of tetrameric Ptch1 in complex with ShhNp (form II). Determined by electron microscopy at 6.5 Å resolution. Released 29 May 2019.

Method: Electron microscopy
Resolution: 6.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 34,484
Mol. weight: 650.74 kDa
Ligands: NAG, CLR, ZN, CA
Released: 29 May 2019

Explore 6N7K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N7K contains 200 α-helices and 106 β-strands across 6 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.

Chains A and D: 45 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	75-96	22
α-helix	98-113	16
α-helix	137-142	6
β-strand	156-161	6	1
α-helix	172-184	13
β-strand	190	1	2
β-strand	197	1	2
α-helix	199-202	4
α-helix	215-222	8
β-strand	228-229	2	1
α-helix	231-234	4
α-helix	238-241	4
α-helix	261-270	10
α-helix	276-284	9
β-strand	326	1	3
β-strand	338	1	3
α-helix	339-342	4
β-strand	343	1	1
β-strand	346-348	3	4
β-strand	354-357	4	4
β-strand	360-364	5	1
α-helix	369-375	7
α-helix	389-409	21
β-strand	418-421	4	1
α-helix	426-434	9
α-helix	439-454	16
α-helix	468-491	24
α-helix	499-502	4
α-helix	504-523	20
α-helix	535-543	9
α-helix	548-561	14
α-helix	568-591	24
α-helix	593-604	12
α-helix	730-745	16
α-helix	751-770	20
β-strand	773	1	5
α-helix	777-779	3
α-helix	786-797	12
β-strand	801-808	8	6
α-helix	817-825	9
α-helix	840-843	4
α-helix	844-863	20
α-helix	872-874	3
α-helix	878-887	10
β-strand	889	1	7
β-strand	897	1	7
β-strand	908-909	2	8
β-strand	913-914	2	8
α-helix	919-929	11
α-helix	931-936	6
α-helix	944-947	4
β-strand	972-978	7	6
α-helix	984-1003	20
β-strand	1007-1009	3	6
α-helix	1013-1017	5
α-helix	1025-1045	21
α-helix	1050-1074	25
β-strand	1078	1	5
α-helix	1081-1105	25
α-helix	1112-1121	10
α-helix	1124-1140	17
α-helix	1146-1151	6
α-helix	1154-1165	12
α-helix	1166-1170	5
α-helix	1171-1177	7

Chains B and E: 50 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	77-96	20
α-helix	101-111	11
α-helix	125-129	5
α-helix	139-146	8
β-strand	152	1	9
β-strand	153-154	2	10
β-strand	157-162	6	11
α-helix	172-186	15
β-strand	190	1	12
β-strand	197	1	12
α-helix	199-201	3
β-strand	203	1	10
α-helix	216-220	5
β-strand	229	1	13
α-helix	232-234	3
α-helix	236-241	6
α-helix	261-271	11
α-helix	277-284	8
α-helix	316-318	3
β-strand	343	1	11
β-strand	348	1	14
β-strand	354	1	14
β-strand	360-361	2	11
β-strand	363	1	13
β-strand	366-367	2	10
α-helix	369-375	7
α-helix	390-408	19
β-strand	417-422	6	11
α-helix	424-434	11
α-helix	439-454	16
α-helix	468-490	23
α-helix	503-510	8
α-helix	513-523	11
α-helix	537-542	6
α-helix	545-562	18
α-helix	568-586	19
α-helix	587-591	5
α-helix	593-600	8
α-helix	601-605	5
α-helix	733-744	12
α-helix	747-767	21
β-strand	772-773	2	15
α-helix	786-797	12
β-strand	801-807	7	16
α-helix	817-827	11
β-strand	832	1	16
α-helix	840-842	3
α-helix	844-865	22
α-helix	873-875	3
α-helix	880-888	9
α-helix	902-905	4
β-strand	908	1	17
α-helix	913	1
β-strand	914	1	17
α-helix	915	1
α-helix	919-927	9
α-helix	966-969	4
β-strand	975-978	4	16
α-helix	984-1003	20
β-strand	1008-1011	4	16
α-helix	1013-1015	3
α-helix	1019-1021	3
α-helix	1025-1045	21
α-helix	1050-1074	25
β-strand	1077-1078	2	15
α-helix	1080-1105	26
α-helix	1113-1137	25
α-helix	1138-1142	5
α-helix	1149-1153	5
α-helix	1154-1164	11
α-helix	1165-1169	5
α-helix	1170-1176	7

Chains C and F: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	9
α-helix	40-42	3
β-strand	47	1	18
β-strand	56	1	19
β-strand	58-59	2	19
α-helix	72-75	4
β-strand	77-78	2	20
β-strand	85-86	2	18
β-strand	97-98	2	20
α-helix	100-116	17
β-strand	123-126	4	18
α-helix	139-142	4
β-strand	145-149	5	18
α-helix	159-167	9
β-strand	172-174	3	18
β-strand	181-184	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1	A, B, D, E	protein	1349	Homo sapiens	Q13635 (AlphaFold model)
Sonic hedgehog protein	C, F	protein	174	Homo sapiens	Q15465 (AlphaFold model)

Sequence of entity 1 (A, B, D, E), FASTA

>6N7K_1 Protein patched homolog 1 (chains A, B, D, E)
MADYKDDDDKSGPDEVDASGRMASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGL
RRAAAPDRDYLHRPSYCDAAFALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCG
KFLVVGLLIFGAFAVGLKAANLETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMI
QTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQI
IEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWE
EMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQE
ELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAW
QRTYVEVVHQSVAQNSTQKVLSFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLR
WDCSKSQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLA
HAFSETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAV
VVVFNFAMVLLIFPAILSMDLYRREDRRLDIFCCFTSPCVSRVIQVEPQAYTDTHDNTRY
SPPPPYSSHSFAHETQITMQSTVQLRTEYDPHTHVYYTTAEPRSEISVQPVTVTQDTLSC
QSPESTSSTRDLLSQFSDSSLHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLG
LLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLL
YDLHRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDD
GVLAYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQA
NIRPHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICS
NYTSLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMV
LALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLAL
EHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFG
PYPEVSPANGLNRLPTPSPEPPPSVVRFAMPPGHTHSGSDSSDSEYSSQTTVSGLSEELR
HYEAQQGAGGPAHQVIVEATENPVFAHSTVVHPESRHHPPSNPRQQPHLDSGSLPPGRQG
QQPRRDLEGSDEVDAVEGSHHHHHHHHHH

Sequence of entity 2 (C, F), FASTA

>6N7K_2 Sonic hedgehog protein (chains C, F)
CGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPD
IIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEG
RAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	20
CLR	Cholesterol	C27 H46 O	10
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	4
PLM	Palmitic acid	C16 H32 O2	2

Primary citation

Inhibition of tetrameric Patched1 by Sonic Hedgehog through an asymmetric paradigm. Qian, H., Cao, P., Hu, M. et al. Nat Commun (2019) 10:2320-2320. DOI 10.1038/s41467-019-10234-9 · 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
6OEV 3.8 Å, Structure of human Patched1 in complex with native Sonic Hedgehog

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