6RMG: PTCH1

Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II. Determined by electron microscopy at 3.4 Å resolution. Released 9 Oct 2019.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Homo sapiens, Eimeria acervulina
Chains: 2
Atoms: 9,810
Mol. weight: 203.19 kDa
Ligands: NAG, Y01, ZN
Released: 9 Oct 2019

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

Secondary structure: helices and β-sheets

6RMG contains 70 α-helices and 32 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: 65 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	48-51	4
α-helix	58-67	10
β-strand	71	1	1
α-helix	78-96	19
α-helix	99-113	15
α-helix	114-118	5
β-strand	121	1	2
α-helix	125-128	4
α-helix	135-146	12
β-strand	154-161	8	3
α-helix	172-186	15
β-strand	190	1	4
β-strand	197	1	4
α-helix	199-202	4
β-strand	203	1	3
α-helix	215-222	8
β-strand	228-229	2	3
α-helix	231-233	3
α-helix	236-241	6
α-helix	256-258	3
α-helix	261-270	10
α-helix	276-284	9
α-helix	290-293	4
β-strand	326-328	3	5
β-strand	336-338	3	5
α-helix	339-342	4
β-strand	343-344	2	3
β-strand	347-349	3	6
α-helix	350-352	3
β-strand	353-356	4	6
β-strand	359-366	8	3
α-helix	369-375	7
α-helix	389-408	20
β-strand	418-422	5	3
α-helix	426-434	9
α-helix	439-457	19
α-helix	467-490	24
α-helix	493-494	2
β-strand	495	1	2
α-helix	503-511	9
α-helix	512-514	3
α-helix	515-523	9
α-helix	536-543	8
α-helix	546-553	8
α-helix	556-561	6
α-helix	568-573	6
α-helix	576-590	15
α-helix	592-604	13
α-helix	732-735	4
α-helix	736-740	5
α-helix	741-744	4
α-helix	747-769	23
β-strand	773	1	7
α-helix	782	1
α-helix	788-796	9
β-strand	801-808	8	8
α-helix	812-814	3
α-helix	816-825	10
α-helix	826-828	3
α-helix	840-842	3
α-helix	844-863	20
α-helix	880-887	8
β-strand	889	1	9
β-strand	897	1	9
α-helix	899-901	3
β-strand	908	1	10
α-helix	910-912	3
α-helix	913	1
β-strand	914	1	10
α-helix	915	1
α-helix	919-929	11
α-helix	931-936	6
α-helix	945-947	3
α-helix	963-965	3
α-helix	967-969	3
β-strand	972-978	7	8
α-helix	984-1004	21
β-strand	1007-1011	5	8
α-helix	1013-1016	4
α-helix	1017-1019	3
α-helix	1024-1047	24
α-helix	1051-1074	24
β-strand	1078	1	7
α-helix	1081-1102	22
α-helix	1111-1120	10
α-helix	1124-1137	14
α-helix	1138-1140	3
α-helix	1153-1167	15
α-helix	1170-1177	8
β-strand	1185	1	1

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	72-75	4
β-strand	77	1	11
β-strand	84-86	3	12
β-strand	98	1	11
α-helix	100-113	14
β-strand	122-126	5	12
α-helix	139-142	4
β-strand	145-150	6	12
α-helix	155-157	3
α-helix	158-168	11
β-strand	172-174	3	12
β-strand	181-184	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1,GFP-like fluorescent chromoprotein FP506, related	A	protein	1471	Homo sapiens, Eimeria acervulina	Q13635 (AlphaFold model), U6GSR1 (AlphaFold model)
Sonic hedgehog protein	B	protein	285	Homo sapiens	Q15465 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6RMG_1 Protein patched homolog 1,GFP-like fluorescent chromoprotein FP506, related (chains A)
MASAGNAAEPQDRGGGGSGCIGAPGRPAGGGRRRRTGGLRRAAAPDRDYLHRPSYCDAAF
ALEQISKGKATGRKAPLWLRAKFQRLLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLKAAN
LETNVEELWVEVGGRVSRELNYTRQKIGEEAMFNPQLMIQTPKEEGANVLTTEALLQHLD
SALQASRVHVYMYNRQWKLEHLCYKSGELITETGYMDQIIEYLYPCLIITPLDCFWEGAK
LQSGTAYLLGKPPLRWTNFDPLEFLEELKKINYQVDSWEEMLNKAEVGHGYMDRPCLNPA
DPDCPATAPNKNSTKPLDMALVLNGGCHGLSRKYMHWQEELIVGGTVKNSTGKLVSAHAL
QTMFQLMTPKQMYEHFKGYEYVSHINWNEDKAAAILEAWQRTYVEVVHQSVAQNSTQKVL
SFTTTTLDDILKSFSDVSVIRVASGYLLMLAYACLTMLRWDCSKSQGAVGLAGVLLVALS
VAAGLGLCSLIGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNKRIPFEDRTGEC
LKRTGASVALTSISNVTAFFMAALIPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDL
YRREDRRLDIFCCFTSPCVSRVIQVEPQAYTDTHDNTRYSPPPPASSHSFAHETQITMQS
TVQLRTEYDPHTHVYYTTAEPRSEISVQPVTVTQDTLSCQSPESTSSTRDLLSQFSDSSL
HCLEPPCTKWTLSSFAEKHYAPFLLKPKAKVVVIFLFLGLLGVSLYGTTRVRDGLDLTDI
VPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLLYDLHRSFSNVKYVMLEENKQL
PKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDDGVLAYKLLVQTGSRDKPIDIS
QLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIRPHRPEWVHDKADYMPETR
LRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICSNYTSLGLSSYPNGYPFLFWEQ
YIGLRHWLLLFISVVLACTFLVCAVFLLNPWTAGIIVMVLALMTVELFGMMGLIGIKLSA
VPVVILIASVGIGVEFTVHVALAFLTAIGDKNRRAVLALEHMFAPVLDGAVSTLLGVLML
AGSEFDFIVRYFFAVLAILTILGVLNGLVLLPVLLSFFGPYPEVSPANAAALEVLFQGPG
GVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPT
LVTTFGYGLQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTL
VNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLA
DHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKA
ASAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (B), FASTA

>6RMG_2 Sonic hedgehog protein (chains B)
MKKHHHHHHGSGMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRL
MEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGIIGPGRGFGK
RRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKDEENT
GADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSD
RDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
Y01	Cholesterol hemisuccinate	C31 H50 O4	11
ZN	Zinc ion	Zn	1

Primary citation

Structural basis of sterol recognition by human hedgehog receptor PTCH1. Qi, C., Di Minin, G., Vercellino, I. et al. Sci Adv (2019) 5:eaaw6490-eaaw6490. DOI 10.1126/sciadv.aaw6490 · 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
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
6DMB 3.9 Å, Cryo-EM structure of human Ptch1

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