6DMO: Protein patched homolog 1

Cryo-EM structure of human Ptch1 with three mutations L282Q/T500F/P504L. Determined by electron microscopy at 4.1 Å resolution. Released 11 Jul 2018.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Homo sapiens
Chains: 1
Atoms: 7,853
Mol. weight: 151.8 kDa
Ligands: NAG
Released: 11 Jul 2018

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

Secondary structure: helices and β-sheets

6DMO contains 39 α-helices and 17 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: 39 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	75-96	22
α-helix	98-114	17
β-strand	121	1	1
α-helix	131	1
α-helix	137-146	10
β-strand	154-162	9	2
α-helix	172-186	15
β-strand	190-191	2	3
β-strand	196-197	2	3
β-strand	203	1	2
α-helix	216-222	7
β-strand	229	1	2
α-helix	231-234	4
α-helix	236-240	5
α-helix	256-258	3
α-helix	261-270	10
α-helix	277-284	8
β-strand	328	1	4
β-strand	336	1	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	360-366	7	2
α-helix	369-375	7
α-helix	390-410	21
β-strand	417-422	6	2
α-helix	425-432	8
α-helix	439-456	18
α-helix	467-490	24
β-strand	495	1	1
α-helix	499-525	27
α-helix	539-562	24
α-helix	568-603	36
α-helix	732-743	12
α-helix	751-769	19
α-helix	786-797	12
β-strand	801-808	8	6
α-helix	816-828	13
α-helix	844-862	19
α-helix	878-884	7
α-helix	901-904	4
α-helix	920-929	10
α-helix	931-936	6
β-strand	972-978	7	6
α-helix	984-1002	19
β-strand	1007-1012	6	6
α-helix	1013-1018	6
α-helix	1027-1045	19
α-helix	1053-1074	22
α-helix	1082-1105	24
α-helix	1113-1137	25
α-helix	1138-1140	3
α-helix	1147-1165	19
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

>6DMO_1 Protein patched homolog 1 (chains A)
MADYKDDDDKSGPDEVDASGRMASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGL
RRAAAPDRDYLHRPSYCDAAFALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCG
KFLVVGLLIFGAFAVGLKAANLETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMI
QTPKEEGANVLTTEALLQHLDSALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQI
IEYLYPCLIITPLDCFWEGAKLQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWE
EMQNKAEVGHGYMDRPCLNPADPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQE
ELIVGGTVKNSTGKLVSAHALQTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAW
QRTYVEVVHQSVAQNSTQKVLSFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLR
WDCSKSQGAVGLAGVLLVALSVAAGLGLCSLIGISFNAATFQVLLFLALGVGVDDVFLLA
HAFSETGQNKRIPFEDRTGECLKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAV
VVVFNFAMVLLIFPAILSMDLYRREDRRLDIFCCFTSPCVSRVIQVEPQAYTDTHDNTRY
SPPPPYSSHSFAHETQITMQSTVQLRTEYDPHTHVYYTTAEPRSEISVQPVTVTQDTLSC
QSPESTSSTRDLLSQFSDSSLHCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLG
LLGVSLYGTTRVRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLL
YDLHRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDD
GVLAYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQA
NIRPHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICS
NYTSLGLSSYPNGYPFLFWEQYIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMV
LALMTVELFGMMGLIGIKLSAVPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLAL
EHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFG
PYPEVSPANGLNRLPTPSPEPPPSVVRFAMPPGHTHSGSDSSDSEYSSQTTVSGLSEELR
HYEAQQGAGGPAHQVIVEATENPVFAHSTVVHPESRHHPPSNPRQQPHLDSGSLPPGRQG
QQPRRDLEGSDEVDAVEGSHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
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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