4Y5V: Diabody 305 complex with EpoR

Diabody 305 complex with EpoR. Determined by X-ray diffraction at 2.6 Å resolution. Released 29 Apr 2015.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 9
Atoms: 10,298
Mol. weight: 154.72 kDa
Released: 29 Apr 2015

Explore 4Y5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y5V contains 42 α-helices and 129 β-strands across 9 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, D and G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
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	112-116	5	2

Chains B, E and H: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4	1	3
β-strand	5	1	4
β-strand	9-12	4	5
β-strand	18-23	6	4
β-strand	35-40	6	5
β-strand	47-50	4	5
β-strand	51	1	6
β-strand	55	1	6
β-strand	64-69	6	4
β-strand	72-77	6	4
α-helix	82-84	3
β-strand	87-93	7	5
β-strand	99-101	3	5
β-strand	102	1	3
β-strand	105-109	5	5

Chain C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	27-29	3	7
β-strand	30	1	8
β-strand	37-42	6	7
β-strand	53-59	7	9
α-helix	63-64	2
β-strand	65-67	3	9
β-strand	69-73	5	7
β-strand	79-84	6	7
α-helix	87-89	3
β-strand	96-102	7	9
β-strand	107-113	7	9
α-helix	115-117	3
β-strand	119	1	8
α-helix	121-124	4
β-strand	125-131	7	10
β-strand	138-143	6	10
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-162	9	11
β-strand	169-174	6	11
β-strand	180-183	4	10
α-helix	186-187	2
β-strand	191-200	10	11
β-strand	207	1	8
β-strand	216-219	4	11

Chain F: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	27-29	3	18
β-strand	30	1	19
β-strand	37-42	6	18
β-strand	53-59	7	20
α-helix	63-64	2
β-strand	65-67	3	20
β-strand	70-74	5	18
β-strand	78-84	7	18
α-helix	87-89	3
β-strand	96-102	7	20
β-strand	107-113	7	20
α-helix	115-117	3
β-strand	119	1	19
α-helix	121-124	4
β-strand	125-131	7	21
β-strand	138-143	6	21
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-161	8	22
β-strand	169-174	6	22
β-strand	180-183	4	21
α-helix	186-187	2
β-strand	191-200	10	22
β-strand	207	1	19
β-strand	216-219	4	22

Chain I: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	27-29	3	29
β-strand	30	1	30
β-strand	37-42	6	29
β-strand	53-59	7	31
α-helix	63-64	2
β-strand	65-67	3	31
β-strand	70-73	4	29
β-strand	79-84	6	29
α-helix	87-89	3
β-strand	96-102	7	31
β-strand	107-113	7	31
α-helix	115-117	3
β-strand	119	1	30
α-helix	121-124	4
β-strand	125-130	6	32
β-strand	138-143	6	32
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-161	8	33
β-strand	170-174	5	33
β-strand	180-183	4	32
β-strand	192-200	9	33
β-strand	207	1	30
α-helix	211-215	5
β-strand	216-218	3	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
diabody 305 VH domain	A, D, G	protein	130	Homo sapiens
Diabody 305 VL domain	B, E, H	protein	117	Homo sapiens
Erythropoietin receptor	C, F, I	protein	229	Homo sapiens	P19235 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>4Y5V_1 diabody 305 VH domain (chains A, D, G)
HSAFAGSEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVANIKP
DGSEKYYVDSVKGRFTISRDNAKNSVYLQMNSLRAEDTAVYYCARVSRGGSYSDWGQGTL
VTVSSGGGGS

Sequence of entity 2 (B, E, H), FASTA

>4Y5V_2 Diabody 305 VL domain (chains B, E, H)
SQSALTQPASVSGSPGQSITISCTGTSSDVGGYIYVSWYQQHPGKAPKLMIYDVSRRPSG
ISDRFSGSKSGNTASLTISGLQAEDEADYYCNSYTTLSTWLFGGGTKVTVLAAAGGG

Sequence of entity 3 (C, F, I), FASTA

>4Y5V_3 Erythropoietin receptor (chains C, F, I)
FAGSADPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGQYSFSYQLEDE
PWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLD
APVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECV
LSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLDKEKAAA

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
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…
4Y5Y 2.85 Å, Diabody 330 complex with EpoR
6MOF 2.89 Å, Monomeric DARPin G2 complex with EpoR

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