6DMB: Human Ptch1

Cryo-EM structure of human Ptch1. Determined by electron microscopy at 3.9 Å resolution. Released 11 Jul 2018.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 7,945
Mol. weight: 152.69 kDa
Ligands: Y01, NAG
Released: 11 Jul 2018

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

Secondary structure: helices and β-sheets

6DMB contains 50 α-helices and 19 β-strands across 1 chain. 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: 50 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	75-95	21
α-helix	98-114	17
α-helix	115-118	4
α-helix	125-128	4
α-helix	137-146	10
β-strand	154	1	1
β-strand	157-162	6	2
α-helix	172-184	13
β-strand	190-191	2	3
β-strand	196-197	2	3
α-helix	217-221	5
β-strand	229	1	2
α-helix	231-233	3
α-helix	237-239	3
α-helix	256-258	3
α-helix	261-270	10
α-helix	278-284	7
α-helix	316-318	3
β-strand	328-331	4	4
β-strand	335-336	2	4
α-helix	339-342	4
β-strand	343	1	2
β-strand	347-348	2	5
β-strand	354-356	3	5
β-strand	360-363	4	2
β-strand	366	1	1
α-helix	369-375	7
α-helix	389-410	22
β-strand	417-421	5	2
α-helix	426-435	10
α-helix	440-456	17
α-helix	471-490	20
α-helix	499-502	4
α-helix	503-505	3
α-helix	507-525	19
α-helix	540-563	24
α-helix	568-604	37
α-helix	732-740	9
α-helix	741-744	4
α-helix	747-749	3
α-helix	751-769	19
α-helix	782	1
α-helix	786-797	12
β-strand	801-807	7	6
α-helix	816-827	12
α-helix	841-843	3
α-helix	844-862	19
α-helix	878-887	10
β-strand	889	1	7
β-strand	897	1	7
α-helix	900-902	3
α-helix	920-929	10
α-helix	931-936	6
α-helix	944-945	2
β-strand	972	1	6
β-strand	975-978	4	6
α-helix	985-1003	19
β-strand	1008-1012	5	6
α-helix	1013-1017	5
α-helix	1018-1021	4
α-helix	1027-1045	19
α-helix	1053-1074	22
α-helix	1081-1105	25
α-helix	1113-1121	9
α-helix	1124-1137	14
α-helix	1147-1154	8
α-helix	1156-1165	10
α-helix	1166-1170	5
α-helix	1171-1177	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1	A	protein	1349	Homo sapiens	Q13635 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6DMB_1 Protein patched homolog 1 (chains A)
MADYKDDDDKSGPDEVDASGRMASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGL
RRAAAPDRDYLHRPSYCDAAFALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCG
KFLVVGLLIFGAFAVGLKAANLETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMI
QTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQI
IEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWE
EMLNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQE
ELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAW
QRTYVEVVHQSVAQNSTQKVLSFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLR
WDCSKSQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLA
HAFSETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAV
VVVFNFAMVLLIFPAILSMDLYRREDRRLDIFCCFTSPCVSRVIQVEPQAYTDTHDNTRY
SPPPPYSSHSFAHETQITMQSTVQLRTEYDPHTHVYYTTAEPRSEISVQPVTVTQDTLSC
QSPESTSSTRDLLSQFSDSSLHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLG
LLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLL
YDLHRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDD
GVLAYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQA
NIRPHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICS
NYTSLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMV
LALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLAL
EHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFG
PYPEVSPANGLNRLPTPSPEPPPSVVRFAMPPGHTHSGSDSSDSEYSSQTTVSGLSEELR
HYEAQQGAGGPAHQVIVEATENPVFAHSTVVHPESRHHPPSNPRQQPHLDSGSLPPGRQG
QQPRRDLEGSDEVDAVEGSHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Structural basis for the recognition of Sonic Hedgehog by human Patched1. Gong, X., Qian, H., Cao, P. et al. Science (2018) 361. DOI 10.1126/science.aas8935 · 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

Browse structure collections

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