6RVD: Protein patched homolog 1

Revised cryo-EM structure of the human 2:1 Ptch1-Shh complex. Determined by electron microscopy at 3.5 Å resolution. Released 2 Oct 2019.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 17,169
Mol. weight: 344.94 kDa
Ligands: CA, ZN, PLM, NAG
Released: 2 Oct 2019

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

Secondary structure: helices and β-sheets

6RVD contains 114 α-helices and 74 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: 53 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	75-96	22
α-helix	100-114	15
α-helix	115-117	3
β-strand	121	1	1
α-helix	125-127	3
α-helix	134-145	12
α-helix	149-151	3
β-strand	152-153	2	2
β-strand	155-162	8	3
α-helix	172-186	15
β-strand	190-192	3	4
β-strand	195-197	3	4
α-helix	199-201	3
α-helix	216-221	6
α-helix	225-226	2
β-strand	228-229	2	3
α-helix	236-238	3
β-strand	246	1	5
β-strand	254	1	5
α-helix	261-270	10
α-helix	276-284	9
α-helix	295-296	2
α-helix	316-317	2
α-helix	319-323	5
β-strand	328	1	6
β-strand	336	1	6
β-strand	343-348	6	3
β-strand	354-365	12	3
α-helix	369-375	7
α-helix	389-408	20
β-strand	417-422	6	3
α-helix	424-434	11
α-helix	439-456	18
α-helix	467-490	24
β-strand	495	1	1
α-helix	497-501	5
α-helix	503-528	26
α-helix	537-562	26
α-helix	568-590	23
α-helix	592-605	14
α-helix	734-740	7
α-helix	747-769	23
β-strand	773	1	7
α-helix	777-780	4
α-helix	786-797	12
β-strand	801-807	7	8
α-helix	817-824	8
β-strand	832	1	8
β-strand	835	1	9
β-strand	839	1	9
α-helix	844-865	22
α-helix	878-887	10
β-strand	889	1	10
β-strand	896	1	10
α-helix	898-901	4
β-strand	908	1	11
α-helix	913	1
β-strand	914	1	11
α-helix	915	1
α-helix	919-929	11
α-helix	931-936	6
β-strand	942	1	12
α-helix	944-947	4
α-helix	962-969	8
β-strand	971	1	12
β-strand	972-978	7	8
α-helix	984-1004	21
β-strand	1008-1012	5	8
α-helix	1013-1017	5
α-helix	1024-1046	23
α-helix	1050-1074	25
β-strand	1078	1	7
α-helix	1080-1092	13
α-helix	1094-1105	12
α-helix	1111-1122	12
α-helix	1124-1138	15
α-helix	1146-1148	3
α-helix	1149-1153	5
α-helix	1154-1163	10
α-helix	1164-1170	7
α-helix	1171-1177	7

Chain B: 53 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	78-96	19
α-helix	98-114	17
α-helix	115-117	3
β-strand	121	1	13
α-helix	125-128	4
α-helix	136-146	11
β-strand	153-162	10	14
α-helix	172-186	15
β-strand	190-192	3	15
β-strand	195-197	3	15
β-strand	203	1	14
α-helix	214-220	7
β-strand	228-229	2	14
α-helix	231-234	4
α-helix	236-241	6
β-strand	246	1	16
α-helix	253	1
β-strand	254	1	16
α-helix	261-270	10
α-helix	276-284	9
α-helix	295-296	2
α-helix	316-317	2
β-strand	328	1	17
β-strand	336	1	17
β-strand	343-344	2	14
β-strand	347-348	2	18
β-strand	354-356	3	18
β-strand	359-367	9	14
α-helix	368	1
α-helix	369-375	7
β-strand	379	1	19
α-helix	389-408	20
β-strand	417-422	6	14
α-helix	424-434	11
α-helix	439-456	18
α-helix	467-490	24
α-helix	493-494	2
β-strand	495	1	13
α-helix	496	1
α-helix	497-528	32
α-helix	537-560	24
α-helix	568-586	19
α-helix	587-591	5
α-helix	592-604	13
α-helix	737-740	4
α-helix	741-743	3
α-helix	747-769	23
β-strand	773	1	20
β-strand	782	1	21
α-helix	786-797	12
β-strand	801-805	5	22
α-helix	816-825	10
β-strand	832	1	22
α-helix	833-834	2
β-strand	835	1	23
β-strand	839	1	23
α-helix	844-865	22
α-helix	878-888	11
β-strand	889	1	24
β-strand	896	1	24
α-helix	899-901	3
β-strand	906	1	25
β-strand	908	1	25
β-strand	914	1	25
α-helix	919-929	11
α-helix	931-936	6
β-strand	942	1	26
α-helix	944-947	4
α-helix	963-969	7
β-strand	971	1	26
β-strand	974-978	5	22
α-helix	984-1004	21
β-strand	1010-1012	3	22
α-helix	1013-1017	5
α-helix	1019-1021	3
α-helix	1024-1047	24
α-helix	1050-1074	25
β-strand	1078	1	20
α-helix	1080-1106	27
α-helix	1111-1137	27
α-helix	1138-1140	3
β-strand	1145	1	21
α-helix	1146-1148	3
α-helix	1149-1153	5
α-helix	1154-1164	11
α-helix	1165-1170	6
α-helix	1171-1177	7

Chain C: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	2
α-helix	33-38	6
α-helix	40-43	4
β-strand	44	1	19
β-strand	47-48	2	27
β-strand	55	1	28
β-strand	59	1	28
α-helix	71-75	5
β-strand	77-78	2	29
β-strand	84-86	3	27
α-helix	94-96	3
β-strand	97-98	2	29
α-helix	100-116	17
β-strand	122-126	5	27
α-helix	139-142	4
β-strand	145-150	6	27
α-helix	155-157	3
α-helix	158-166	9
β-strand	172-174	3	27
β-strand	181-184	4	27

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

>6RVD_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

>6RVD_2 Sonic hedgehog protein (chains C)
CGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPD
IIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEG
RAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	1
PLM	Palmitic acid	C16 H32 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7
CLR	Cholesterol	C27 H46 O	4

Primary citation

The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism. Rudolf, A.F., Kinnebrew, M., Kowatsch, C. et al. Nat Chem Biol (2019) 15:975-982. DOI 10.1038/s41589-019-0370-y · 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
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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