6RVC: Patched-1 ectodomain 2

Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75. Determined by X-ray diffraction at 2.2 Å resolution. Released 2 Oct 2019.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 5,347
Mol. weight: 136.98 kDa
Ligands: NAG
Released: 2 Oct 2019

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

Secondary structure: helices and β-sheets

6RVC contains 27 α-helices and 51 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 B: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	844-864	21
β-strand	869	1	1
β-strand	872	1	1
α-helix	878-887	10
β-strand	889	1	2
β-strand	897	1	2
α-helix	899-903	5
β-strand	908	1	3
β-strand	914	1	3
α-helix	919-929	11
α-helix	931-934	4

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	844-864	21
β-strand	869	1	7
β-strand	872	1	7
α-helix	878-887	10
β-strand	889	1	8
β-strand	897	1	8
α-helix	901-904	4
β-strand	908	1	9
β-strand	914	1	9
α-helix	919-929	11
α-helix	931-934	4

Chains D, E and F: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	18-24	7	10
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	11
α-helix	108-110	3
β-strand	111-114	4	11
β-strand	118-123	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein patched homolog 1	A, B, C	protein	261	Homo sapiens	Q13635 (AlphaFold model)
Nanobody NB75	D, E, F	protein	134	Lama glama

Sequence of entity 1 (A, B, C), FASTA

>6RVC_1 Protein patched homolog 1 (chains A, B, C)
ETGHHHHHHRDGLDLTDIVPRETREYDFIAAQFKYFSFYNMYIVTQKADYPNIQHLLYDL
HRSFSNVKYVMLEENKQLPKMWLHYFRDWLQGLQDAFDSDWETGKIMPNNYKNGSDDGVL
AYKLLVQTGSRDKPIDISQLTKQRLVDADGIINPSAFYIYLTAWVSNDPVAYAASQANIR
PHRPEWVHDKADYMPETRLRIPAAEPIEYAQFPFYLNGLRDTSDFVEAIEKVRTICSNYT
SLGLSSYPNGYPFLFWEQYIG

Sequence of entity 2 (D, E, F), FASTA

>6RVC_2 Nanobody NB75 (chains D, E, F)
QVQLQESGGGLVQAGDSLTLSCAASGRTFSSYTMGWFRQAPGKERDFIAGITSTGSSTYY
ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTADYYCARKVAGGSYYQKDKYDYWGQGTQV
TVSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (SO4) are not listed.

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
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
6DMB 3.9 Å, Cryo-EM structure of human Ptch1

Browse structure collections

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