6VG4: Human protocadherin 10 ectodomain

Human protocadherin 10 ectodomain. Determined by X-ray diffraction at 3.3 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,157
Mol. weight: 75.53 kDa
Ligands: CA, MAN, TAM
Released: 11 Mar 2020

Explore 6VG4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VG4 contains 20 α-helices and 55 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: 20 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
α-helix	11-12	2
β-strand	16-19	4	2
α-helix	20-24	5
α-helix	30-34	5
β-strand	37-38	2	1
β-strand	47-50	4	2
β-strand	55-58	4	2
α-helix	64-67	4
β-strand	75-82	8	1
β-strand	87-96	10	1
α-helix	97	1
β-strand	104	1	3
β-strand	109-115	7	4
α-helix	118-119	2
β-strand	123-125	3	5
α-helix	127-129	3
β-strand	130	1	3
α-helix	135-137	3
β-strand	139-144	6	4
β-strand	150-152	3	5
β-strand	155-156	2	6
β-strand	162-163	2	6
β-strand	165-168	4	5
β-strand	179-188	10	4
β-strand	214-224	11	4
β-strand	232-233	2	7
β-strand	237-243	7	8
α-helix	246-247	2
β-strand	251-254	4	9
β-strand	257-258	2	7
α-helix	263-266	4
β-strand	268-272	5	8
α-helix	278-283	6
β-strand	284-286	3	9
β-strand	292-295	4	9
β-strand	306-315	10	8
β-strand	323-332	10	8
α-helix	333	1
β-strand	340-346	7	10
β-strand	349-351	3	11
α-helix	354-355	2
β-strand	359-366	8	10
α-helix	371-374	4
β-strand	376-381	6	11
β-strand	386-390	5	10
β-strand	395-400	6	10
β-strand	411-420	10	11
β-strand	427-437	11	11
α-helix	438	1
β-strand	445-446	2	12
β-strand	450-456	7	13
β-strand	463-467	5	14
β-strand	470-471	2	12
α-helix	476-479	4
β-strand	481-485	5	13
α-helix	486-487	2
β-strand	489-490	2	15
β-strand	493-494	2	15
α-helix	495-497	3
β-strand	499-501	3	14
β-strand	507-510	4	14
β-strand	521-530	10	13
β-strand	538-548	11	13
α-helix	554-555	2
β-strand	556-559	4	16
β-strand	569-573	5	17
β-strand	582-585	4	18
β-strand	587-589	3	16
α-helix	594-596	3
β-strand	600-603	4	17
β-strand	612-614	3	18
β-strand	620-623	4	18
β-strand	637-644	8	17
β-strand	652-661	10	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protocadherin-10	A	protein	669	Homo sapiens	Q9P2E7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VG4_1 Protocadherin-10 (chains A)
SQLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNE
KIDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLDINDNPPSFPEPDLTVEISESATP
GTRFPLESAFDPDVGTNSLRDYEITPNSYFSLDVQTQGDGNRFAELVLEKPLDREQQAVH
RYVLTAVDGGGGGGVGEGGGGGGGAGLPPQQQRTGTALLTIRVLDSNDNVPAFDQPVYTV
SLPENSPPGTLVIQLNATDPDEGQNGEVVYSFSSHISPRARELFGLSPRTGRLEVSGELD
YEESPVYQVYVQAKDLGPNAVPAHCKVLVRVLDANDNAPEISFSTVKEAVSEGAAPGTVV
ALFSVTDRDSEENGQVQCELLGDVPFRLKSSFKNYYTIVTEAPLDREAGDSYTLTVVARD
RGEPALSTSKSIQVQVSDVNDNAPRFSQPVYDVYVTENNVPGAYIYAVSATDRDEGANAQ
LAYSILECQIQGMSVFTYVSINSENGYLYALRSFDYEQLKDFSFQVEARDAGSPQALAGN
ATVNILIVDQNDNAPAIVAPLPGRNGTPAREVLPRSAEPGYLLTRVAAVDADDGENARLT
YSIVRGNEMNLFRMDWRTGELRTARRVPAKRDPQRPYELVIEVRDHGQPPLSSTATLVVQ
LVDHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	15
MAN	alpha-D-mannopyranose	C6 H12 O6	3
TAM	Tris(hydroxyethyl)aminomethane	C7 H17 N O3	1

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered delta-Protocadherins. Harrison, O.J., Brasch, J., Katsamba, P.S. et al. Cell Rep (2020) 30:2655-2671.e7. DOI 10.1016/j.celrep.2020.02.003 · PubMed

Other PDB entries of the same protein (UniProt Q9P2E7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6VFQ 2.3 Å, Crystal structure of monomeric human protocadherin 10 EC1-EC4
9L41 2.99 Å, Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human…
9DQV 3.3 Å, Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
9L1N 3.3 Å, Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human…
6VFW 3.6 Å, Crystal structure of human delta protocadherin 10 EC1-EC4
9E96 4.05 Å, WEEV CBA87 VLP in complex with human PCDH10-EC1

Browse structure collections

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