5IRY: Human Desmocollin-1 ectodomain

Crystal structure of human Desmocollin-1 ectodomain. Determined by X-ray diffraction at 3.1 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 8,722
Mol. weight: 127.25 kDa
Ligands: MAN, CA, NAG
Released: 22 Jun 2016

Explore 5IRY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IRY contains 28 α-helices and 98 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: 14 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	3-6	4
β-strand	7-10	4	2
β-strand	19-23	5	3
β-strand	26	1	4
α-helix	27-29	3
β-strand	35-39	5	2
β-strand	51-53	3	3
β-strand	59-62	4	3
β-strand	73-81	9	2
β-strand	92-99	8	2
β-strand	107-108	2	5
β-strand	112-118	7	6
α-helix	121-122	2
β-strand	126-129	4	7
β-strand	132-133	2	5
β-strand	146-153	8	6
β-strand	160-162	3	7
β-strand	168-171	4	7
β-strand	183-191	9	6
α-helix	193-195	3
β-strand	201-211	11	6
α-helix	212	1
β-strand	219-220	2	8
β-strand	225-230	6	9
β-strand	236-241	6	10
β-strand	243-244	2	8
β-strand	256-262	7	9
β-strand	269-273	5	10
α-helix	279	1
β-strand	280-284	5	10
β-strand	295-304	10	9
β-strand	321-329	9	9
α-helix	330	1
β-strand	336	1	11
β-strand	341-347	7	12
α-helix	350-351	2
β-strand	355-356	2	13
α-helix	359-361	3
β-strand	362	1	11
α-helix	363	1
β-strand	376	1	12
β-strand	384-386	3	13
β-strand	393-395	3	13
α-helix	398-399	2
β-strand	407	1	12
β-strand	410-415	6	12
β-strand	418	1	14
β-strand	424	1	14
β-strand	427-434	8	12
α-helix	435	1
β-strand	442	1	15
β-strand	448-449	2	16
β-strand	456-459	4	17
β-strand	462	1	15
α-helix	471	1
α-helix	473	1
β-strand	474-477	4	16
β-strand	485-488	4	17
β-strand	495-499	5	17
β-strand	507-515	9	16
β-strand	521-530	10	16

Chain B: 14 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	4
α-helix	3-6	4
β-strand	7-10	4	18
α-helix	16	1
β-strand	19-23	5	19
β-strand	26	1	1
α-helix	27-29	3
β-strand	35-39	5	18
β-strand	41	1	20
β-strand	45	1	20
β-strand	51-53	3	19
β-strand	59-62	4	19
β-strand	73-81	9	18
β-strand	92-99	8	18
β-strand	107-108	2	21
β-strand	112-118	7	22
α-helix	121-122	2
β-strand	126-129	4	23
β-strand	132-133	2	21
β-strand	146-153	8	22
β-strand	160-162	3	23
β-strand	168-171	4	23
β-strand	183-191	9	22
α-helix	193-195	3
β-strand	201-211	11	22
α-helix	212	1
β-strand	219-220	2	24
β-strand	225-230	6	25
β-strand	236-241	6	26
β-strand	243-244	2	24
β-strand	256-262	7	25
β-strand	269-273	5	26
α-helix	279	1
β-strand	280-284	5	26
β-strand	295-304	10	25
α-helix	307-308	2
β-strand	321-329	9	25
β-strand	336	1	27
β-strand	341-347	7	28
α-helix	350-351	2
β-strand	355-357	3	29
α-helix	359-361	3
β-strand	362	1	27
β-strand	376	1	28
β-strand	384-386	3	29
β-strand	392-395	4	29
α-helix	398-399	2
β-strand	412-415	4	28
β-strand	418	1	30
β-strand	424	1	30
β-strand	427-434	8	28
α-helix	435	1
β-strand	442	1	31
β-strand	449	1	32
β-strand	458	1	33
β-strand	462	1	31
α-helix	471	1
α-helix	473	1
β-strand	474-477	4	34
β-strand	485-488	4	33
β-strand	496-499	4	33
β-strand	507-515	9	34
β-strand	521-529	9	34
β-strand	530	1	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Desmocollin-1	A, B	protein	548	Homo sapiens	Q08554 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IRY_1 Desmocollin-1 (chains A, B)
RWAPIPASLMENSLGPFPQHVQQIQSDAAQNYTIFYSISGPGVDKEPFNLFYIEKDTGDI
FCTRSIDREKYEQFALYGYATTADGYAPEYPLPLIIKIEDDNDNAPYFEHRVTIFTVPEN
CRSGTSVGKVTATDLDEPDTLHTRLKYKILQQIPDHPKHFSIHPDTGVITTTTPFLDREK
CDTYQLIMEVRDMGGQPFGLFNTGTITISLEDENDNPPSFTETSYVTEVEENRIDVEILR
MKVQDQDLPNTPHSKAVYKILQGNENGNFIISTDPNTNEGVLCVVKPLNYEVNRQVILQV
GVINEAQFSKAASSQTPTMCTTTVTVKIIDSDEGPECHPPVKVIQSQDGFPAGQELLGYK
ALDPEISSGEGLRYQKLGDEDNWFEINQHTGDLRTLKVLDRESKFVKNNQYNISVVAVDA
VGRSCTGTLVVHLDDYNDHAPQIDKEVTICQNNEDFAVLKPVDPDGPENGPPFQFFLDNS
ASKNWNIEEKDGKTAILRQRQNLDYNYYSVPIQIKDRHGLVATHMLTVRVCDCSTPSECR
MKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	9
CA	Calcium ion	Ca	24
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

Structural basis of adhesive binding by desmocollins and desmogleins. Harrison, O.J., Brasch, J., Lasso, G. et al. Proc Natl Acad Sci U S A (2016) 113:7160-7165. DOI 10.1073/pnas.1606272113 · PubMed

Other PDB entries of the same protein (UniProt Q08554 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9A8U Integrative structure of the epithelial desmosomal outer plaque

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