4Y5Y: Diabody 330 complex with EpoR

Diabody 330 complex with EpoR. Determined by X-ray diffraction at 2.85 Å resolution. Released 18 Mar 2015.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,531
Mol. weight: 102.43 kDa
Released: 18 Mar 2015

Explore 4Y5Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y5Y contains 28 α-helices and 88 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.

Chain A: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-11	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
α-helix	101-103	3
β-strand	105-108	4	2
β-strand	112-115	4	2

Chain B: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
β-strand	5	1	4
β-strand	9-12	4	5
β-strand	18-23	6	4
β-strand	29	1	6
β-strand	32	1	6
β-strand	35-40	6	5
β-strand	47-50	4	5
β-strand	51	1	7
β-strand	55	1	7
β-strand	64-69	6	4
β-strand	72-77	6	4
α-helix	82-84	3
β-strand	87-92	6	5
α-helix	96-98	3
β-strand	101-102	2	5
β-strand	103	1	3
β-strand	106-110	5	5

Chain C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
β-strand	27-29	3	8
β-strand	30	1	9
β-strand	37-42	6	8
β-strand	53-59	7	10
α-helix	63-64	2
β-strand	65-67	3	10
β-strand	70-73	4	8
β-strand	79-84	6	8
α-helix	87-89	3
β-strand	96-102	7	10
β-strand	107-113	7	10
α-helix	115-117	3
β-strand	119-120	2	9
α-helix	121-124	4
β-strand	125-131	7	11
β-strand	138-143	6	11
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-162	9	12
β-strand	167-174	8	12
β-strand	180-183	4	11
β-strand	191-200	10	12
β-strand	207-208	2	9
α-helix	209-215	7
β-strand	216-219	4	12

Chain D: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-11	2	14
β-strand	17-25	9	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	46-51	6	14
β-strand	58-60	3	14
α-helix	62-64	3
β-strand	68-73	6	13
β-strand	78-84	7	13
α-helix	88-90	3
β-strand	92-99	8	14
α-helix	101-103	3
β-strand	105-108	4	14
β-strand	112-115	4	14

Chain E: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
β-strand	5	1	16
β-strand	9-12	4	17
β-strand	18-23	6	16
β-strand	35-40	6	17
β-strand	47-50	4	17
β-strand	51	1	18
β-strand	55	1	18
β-strand	64-69	6	16
β-strand	72-77	6	16
α-helix	82-84	3
β-strand	87-92	6	17
α-helix	96-98	3
β-strand	101-102	2	17
β-strand	103	1	15
β-strand	106-110	5	17

Chain F: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
β-strand	27-29	3	19
β-strand	30	1	20
β-strand	37-42	6	19
β-strand	53-59	7	21
α-helix	63-64	2
β-strand	65-67	3	21
β-strand	70-73	4	19
β-strand	79-84	6	19
α-helix	87-89	3
β-strand	96-102	7	21
β-strand	107-113	7	21
α-helix	115-117	3
β-strand	119	1	20
α-helix	121-124	4
β-strand	125-131	7	22
β-strand	138-143	6	22
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-162	9	23
β-strand	167-174	8	23
β-strand	180-183	4	22
β-strand	191-200	10	23
β-strand	207	1	20
α-helix	209-215	7
β-strand	216-219	4	23
α-helix	220-223	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
diabody 330 VH domain	A, D	protein	130	Homo sapiens
diabody 330 VL domain	B, E	protein	117	Homo sapiens
Erythropoietin receptor	C, F	protein	229	Homo sapiens	P19235 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4Y5Y_1 diabody 330 VH domain (chains A, D)
HSAFAGSEVQLVESGGGLVQPGGSLRLSCAVSGFTFSKYWMTWVRQAPGKGLEWVANIKP
DGSEKYYVESVKGRFTISRDNAKNSVYLQMNSVRAEDTAVYYCARVSRGGSFSDWGQGTL
VTVSSGGGGS

Sequence of entity 2 (B, E), FASTA

>4Y5Y_2 diabody 330 VL domain (chains B, E)
QSALTQPPSASGSPGQSVTISCTGTSSDVGAYNYVSWYQQHPGKAPKLMIYEVARRPSGV
PDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYAGSNNFAVFGRGTKLTVLAAAGGG

Sequence of entity 3 (C, F), FASTA

>4Y5Y_3 Erythropoietin receptor (chains C, F)
FAGSADPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGQYSFSYQLEDE
PWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLD
APVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECV
LSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSLDDKEKAAA

Primary citation

Tuning Cytokine Receptor Signaling by Re-orienting Dimer Geometry with Surrogate Ligands. Moraga, I., Wernig, G., Wilmes, S. et al. Cell (2015) 160:1196-1208. DOI 10.1016/j.cell.2015.02.011 · PubMed

Other PDB entries of the same protein (UniProt P19235 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1EER 1.9 Å, Crystal structure of human erythropoietin complexed to its receptor at 1.9 Å
6MOI 2.06 Å, Dimeric DARPin C_angle_R5 complex with EpoR
6MOE 2.09 Å, Monomeric DARPin E2 complex with EpoR
8VUI 2.1 Å, Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin…
1ERN 2.4 Å, Native structure of the extracellular domain of erythropoietin (EPO) receptor [ebp]
6MOJ 2.43 Å, Dimeric DARPin A_angle_R5 complex with EpoR
4Y5V 2.6 Å, Diabody 305 complex with EpoR
6E2Q 2.65 Å, Structure of human JAK2 FERM/SH2 in complex with Erythropoietin Receptor
1EBA 2.7 Å, Complex between the extracellular domain of erythropoietin (EPO) receptor [ebp] and an…
1CN4 2.8 Å, Erythropoietin complexed with extracellular domains of erythropoietin receptor
1EBP 2.8 Å, Complex between the extracellular domain of erythropoietin (EPO) receptor [ebp] and an…
6MOF 2.89 Å, Monomeric DARPin G2 complex with EpoR

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