6VFW: Human delta protocadherin 10 EC1-EC4

Crystal structure of human delta protocadherin 10 EC1-EC4. Determined by X-ray diffraction at 3.6 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 5
Atoms: 16,932
Mol. weight: 250.44 kDa
Ligands: CA, MAN
Released: 11 Mar 2020

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

Secondary structure: helices and β-sheets

6VFW contains 82 α-helices and 164 β-strands across 5 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: 16 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
α-helix	11-12	2
β-strand	16-19	4	2
α-helix	20-24	5
α-helix	28-30	3
α-helix	31-34	4
β-strand	37-38	2	1
α-helix	40-42	3
β-strand	47-50	4	2
β-strand	55-58	4	2
α-helix	61-62	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	150-156	7	5
β-strand	162-168	7	5
β-strand	179-188	10	4
β-strand	214-224	11	4
α-helix	225	1
β-strand	232	1	6
β-strand	237-243	7	7
α-helix	246-247	2
β-strand	251-254	4	8
β-strand	258	1	6
α-helix	263-266	4
β-strand	268-272	5	7
α-helix	278-283	6
β-strand	284-286	3	8
β-strand	292-295	4	8
β-strand	306-315	10	7
β-strand	323-332	10	7
β-strand	340-346	7	9
β-strand	350-351	2	10
β-strand	359-366	8	9
α-helix	371-374	4
β-strand	376-380	5	11
β-strand	386-389	4	9
β-strand	395-400	6	9
β-strand	411-420	10	11
β-strand	427-435	9	11
β-strand	436-437	2	10

Chain B: 18 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	12
α-helix	11-12	2
β-strand	16-19	4	13
α-helix	20-24	5
α-helix	31-34	4
β-strand	37-38	2	12
α-helix	40-42	3
β-strand	47-50	4	13
β-strand	55-58	4	13
α-helix	61-62	2
α-helix	64-67	4
β-strand	75-82	8	12
β-strand	87-96	10	12
α-helix	97	1
β-strand	104	1	14
β-strand	109-115	7	15
α-helix	118-119	2
β-strand	123-125	3	16
α-helix	127-129	3
β-strand	130	1	14
α-helix	135-137	3
β-strand	139-144	6	15
β-strand	150-158	9	16
β-strand	161-168	8	16
β-strand	179-188	10	15
α-helix	209-212	4
β-strand	214-224	11	15
α-helix	225	1
β-strand	237-243	7	17
α-helix	246-247	2
β-strand	251-254	4	18
α-helix	263-266	4
β-strand	268-272	5	17
α-helix	278-283	6
β-strand	284-286	3	18
β-strand	292-295	4	18
β-strand	306-315	10	17
β-strand	323-332	10	17
β-strand	340-346	7	19
β-strand	349-351	3	20
β-strand	359-366	8	19
α-helix	371-374	4
β-strand	376-380	5	20
β-strand	387-389	3	19
β-strand	395-399	5	19
α-helix	403-404	2
β-strand	411-420	10	20
β-strand	427-437	11	20
α-helix	438	1

Chain C: 17 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	21
α-helix	11-12	2
β-strand	16-19	4	22
α-helix	20-24	5
α-helix	28-30	3
α-helix	31-34	4
β-strand	37-38	2	21
α-helix	40-42	3
β-strand	47-50	4	22
β-strand	55-58	4	22
α-helix	61-62	2
α-helix	64-67	4
β-strand	75-82	8	21
β-strand	87-96	10	21
α-helix	97	1
β-strand	104	1	23
β-strand	109-115	7	24
α-helix	118-119	2
β-strand	123-125	3	25
α-helix	127-129	3
β-strand	130	1	23
α-helix	135-137	3
β-strand	139-144	6	24
β-strand	150-156	7	25
β-strand	162-168	7	25
β-strand	179-188	10	24
α-helix	210-212	3
β-strand	214-224	11	24
α-helix	225	1
β-strand	232	1	26
β-strand	237-243	7	27
α-helix	246-247	2
β-strand	251-254	4	28
β-strand	258	1	26
α-helix	263-266	4
β-strand	268-272	5	27
α-helix	278-283	6
β-strand	284-286	3	28
β-strand	292-295	4	28
β-strand	306-315	10	27
β-strand	323-332	10	27
β-strand	340-346	7	29
β-strand	349-351	3	30
β-strand	359-366	8	29
α-helix	371-374	4
β-strand	376-380	5	30
β-strand	386-392	7	29
β-strand	395-400	6	29
β-strand	411-420	10	30
β-strand	427-437	11	30

Chain D: 15 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	31
α-helix	11-12	2
β-strand	16-19	4	32
α-helix	20-24	5
α-helix	28-30	3
β-strand	37-38	2	31
α-helix	40-42	3
β-strand	47-50	4	32
β-strand	55-58	4	32
α-helix	61-62	2
α-helix	64-67	4
β-strand	75-82	8	31
β-strand	87-96	10	31
α-helix	97	1
β-strand	104	1	33
β-strand	109-115	7	34
α-helix	118-119	2
β-strand	123-125	3	35
α-helix	127-129	3
β-strand	130	1	33
α-helix	135-137	3
β-strand	139-144	6	34
β-strand	150-156	7	35
β-strand	162-168	7	35
β-strand	179-188	10	34
β-strand	214-224	11	34
α-helix	225	1
β-strand	232-233	2	36
β-strand	237-243	7	37
α-helix	246-247	2
β-strand	251-254	4	38
β-strand	257-258	2	36
α-helix	263-266	4
β-strand	268-272	5	37
α-helix	278-283	6
β-strand	284-286	3	38
β-strand	292-295	4	38
β-strand	306-315	10	37
β-strand	323-332	10	37
β-strand	340-346	7	39
β-strand	349-351	3	40
β-strand	361-366	6	39
α-helix	371-374	4
β-strand	376-380	5	40
β-strand	387-389	3	39
β-strand	395-399	5	39
β-strand	411-420	10	40
β-strand	427-437	11	40

Chain E: 16 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	41
α-helix	11-12	2
β-strand	16-19	4	42
α-helix	20-24	5
α-helix	28-30	3
α-helix	31-34	4
β-strand	37-38	2	41
α-helix	40-42	3
β-strand	47-50	4	42
β-strand	55-58	4	42
α-helix	61-62	2
α-helix	64-67	4
β-strand	75-82	8	41
β-strand	87-96	10	41
α-helix	97	1
β-strand	104	1	43
β-strand	109-115	7	44
α-helix	118-119	2
β-strand	123-126	4	45
α-helix	127-129	3
β-strand	130	1	43
α-helix	135-137	3
β-strand	139-144	6	44
β-strand	150-156	7	45
β-strand	162-168	7	45
β-strand	179-188	10	44
β-strand	214-224	11	44
α-helix	225	1
β-strand	232	1	46
β-strand	237-243	7	47
α-helix	246-247	2
β-strand	251-254	4	48
β-strand	258	1	46
α-helix	263-266	4
β-strand	268-272	5	47
α-helix	278-283	6
β-strand	284-286	3	48
β-strand	292-295	4	48
β-strand	306-315	10	47
β-strand	323-332	10	47
β-strand	340-346	7	49
β-strand	349-351	3	50
β-strand	359-366	8	49
α-helix	371-374	4
β-strand	376-380	5	50
β-strand	386-389	4	49
β-strand	395-400	6	49
β-strand	411-420	10	50
β-strand	427-437	11	50

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protocadherin-10	A, B, C, D, E	protein	444	Homo sapiens	Q9P2E7 (AlphaFold model)

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

>6VFW_1 Protocadherin-10 (chains A, B, C, D, E)
SQLHYTVQEEQEHGTFVGNIAEDLGLDITKLSARGFQTVPNSRTPYLDLNLETGVLYVNE
KIDREQICKQSPSCVLHLEVFLENPLELFQVEIEVLDINDNPPSFPEPDLTVEISESATP
GTRFPLESAFDPDVGTNSLRDYEITPNSYFSLDVQTQGDGNRFAELVLEKPLDREQQAVH
RYVLTAVDGGGGGGVGEGGGGGGGAGLPPQQQRTGTALLTIRVLDSNDNVPAFDQPVYTV
SLPENSPPGTLVIQLNATDPDEGQNGEVVYSFSSHISPRARELFGLSPRTGRLEVSGELD
YEESPVYQVYVQAKDLGPNAVPAHCKVLVRVLDANDNAPEISFSTVKEAVSEGAAPGTVV
ALFSVTDRDSEENGQVQCELLGDVPFRLKSSFKNYYTIVTEAPLDREAGDSYTLTVVARD
RGEPALSTSKSIQVQVSDHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	45
MAN	alpha-D-mannopyranose	C6 H12 O6	10

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…
6VG4 3.3 Å, Human protocadherin 10 ectodomain
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…
9E96 4.05 Å, WEEV CBA87 VLP in complex with human PCDH10-EC1

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