4Y5X: Diabody 305 complex with EpoR

Diabody 305 complex with EpoR. Determined by X-ray diffraction at 3.15 Å resolution. Released 18 Mar 2015.

Method: X-ray diffraction
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 12
Atoms: 13,334
Mol. weight: 207.05 kDa
Ligands: FLC
Released: 18 Mar 2015

Explore 4Y5X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y5X contains 54 α-helices and 181 β-strands across 12 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: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-40	7	3
β-strand	44-51	8	3
β-strand	58-60	3	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	107	1	4
β-strand	111-113	3	3
β-strand	118-120	3	3
β-strand	121-122	2	2

Chain B: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
β-strand	5	1	6
β-strand	9-12	4	7
β-strand	17-23	7	6
β-strand	34-39	6	7
β-strand	46-49	4	7
β-strand	50	1	8
β-strand	54	1	8
β-strand	63-67	5	6
β-strand	71-77	7	6
α-helix	81-83	3
β-strand	86-92	7	7
β-strand	99-101	3	7
β-strand	102	1	5
β-strand	105-109	5	7

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	27-29	3	9
β-strand	30	1	10
β-strand	37-42	6	9
β-strand	53-59	7	11
α-helix	63-64	2
β-strand	65-67	3	11
β-strand	69-74	6	9
β-strand	78-84	7	9
α-helix	87-89	3
β-strand	92	1	4
β-strand	96-102	7	11
β-strand	107-113	7	11
α-helix	115-117	3
β-strand	119	1	10
α-helix	121-124	4
β-strand	125-130	6	12
β-strand	138-143	6	12
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-161	8	13
β-strand	168-174	7	13
α-helix	175	1
β-strand	180-183	4	12
β-strand	191-200	10	13
α-helix	201	1
β-strand	207	1	10
α-helix	209-215	7
β-strand	216-219	4	13

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-40	7	16
β-strand	44-51	8	16
β-strand	58-60	3	16
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-99	8	16
α-helix	106-108	3
β-strand	111-113	3	16
β-strand	118-120	3	16
β-strand	121-122	2	15

Chain E: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	17
β-strand	5	1	18
β-strand	9-12	4	19
β-strand	18-23	6	18
β-strand	34-39	6	19
β-strand	46-49	4	19
β-strand	50	1	20
β-strand	54	1	20
β-strand	63-67	5	18
β-strand	71-76	6	18
α-helix	81-83	3
β-strand	86-92	7	19
β-strand	99-101	3	19
β-strand	102	1	17
β-strand	105-109	5	19

Chain F: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	27-29	3	21
β-strand	30	1	22
β-strand	36-42	7	21
β-strand	53-59	7	23
α-helix	63-64	2
β-strand	65-67	3	23
β-strand	69-74	6	21
β-strand	78-85	8	21
α-helix	87-89	3
β-strand	96-102	7	23
β-strand	107-113	7	23
α-helix	115-117	3
β-strand	119	1	22
α-helix	121-124	4
β-strand	125-131	7	24
β-strand	138-143	6	24
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-161	8	25
β-strand	168-174	7	25
α-helix	175	1
β-strand	180-183	4	24
β-strand	191-200	10	25
α-helix	201	1
β-strand	207	1	22
α-helix	209-215	7
β-strand	216-219	4	25

Chain G: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	11-12	2	27
β-strand	17-25	9	26
α-helix	29-31	3
β-strand	34-39	6	28
β-strand	45-51	7	28
β-strand	58-60	3	28
β-strand	68-73	6	26
β-strand	78-84	7	26
α-helix	88-90	3
β-strand	92-99	8	28
β-strand	107	1	29
β-strand	111-113	3	28
β-strand	118-120	3	28
β-strand	121-122	2	27

Chain H: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	30
β-strand	5	1	31
β-strand	9-11	3	32
β-strand	17-23	7	31
β-strand	34-39	6	32
β-strand	46-49	4	32
β-strand	50	1	33
β-strand	54	1	33
β-strand	63-67	5	31
β-strand	71-77	7	31
α-helix	81-83	3
β-strand	86-93	8	32
β-strand	98-101	4	32
β-strand	102	1	30
β-strand	105-108	4	32

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
diabody 310 VL domain	A, D, G, J	protein	136	Homo sapiens
diabody 310 VH domain	B, E, H, K	protein	116	Homo sapiens	Q5NV67 (AlphaFold model)
Erythropoietin receptor	C, F, I, L	protein	229	Homo sapiens	P19235 (AlphaFold model)

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

>4Y5X_1 diabody 310 VL domain (chains A, D, G, J)
HSAFAGSEVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISG
SGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCVKDRVAVAGKGSYYFDS
WGRGTTVTVSSGGGGS

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

>4Y5X_2 diabody 310 VH domain (chains B, E, H, K)
QSVLTQPPSVSEAPGQRVTIACSGSSSNIGNNAVSWYQQLPGKAPTLLIYYDNLLPSGVS
DRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNDWVFGGGTKVTVLAAAGGG

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

>4Y5X_3 Erythropoietin receptor (chains C, F, I, L)
FAGSADPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGQYSFSYQLEDE
PWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLD
APVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGQGAGSVQRVEILEGRTECV
LSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLDKEKAAA

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	1

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

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

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