8VUI: FabS1CE-EPR-1, an elbow-locked Fab

Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor. Determined by X-ray diffraction at 2.1 Å resolution. Released 10 Jul 2024.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,016
Mol. weight: 73.71 kDa
Ligands: CIT, NAG
Released: 10 Jul 2024

Explore 8VUI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VUI contains 26 α-helices and 64 β-strands across 3 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: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	12-13	2	2
β-strand	18-26	9	1
α-helix	30-36	3
β-strand	39-44	6	3
β-strand	51-56	6	3
β-strand	65-67	3	3
β-strand	76-81	6	1
β-strand	86-92	7	1
α-helix	96-98	3
β-strand	100-108	9	3
β-strand	114-118	5	3
β-strand	122-124	3	3
β-strand	125-126	2	2
β-strand	131	1	4
α-helix	132-133	2
β-strand	134-138	5	5
β-strand	149-159	11	5
β-strand	160	1	4
β-strand	165-168	4	6
α-helix	169-171	3
β-strand	173	1	6
β-strand	177-179	3	5
α-helix	180-182	3
β-strand	183-184	2	5
β-strand	190-199	10	5
α-helix	200-202	3
β-strand	209-214	6	6
α-helix	215-217	3
β-strand	219-224	6	6
α-helix	227-229	3

Chain D: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-21	13
β-strand	27-29	3	13
β-strand	30	1	14
β-strand	37-42	6	13
α-helix	50-52	3
β-strand	53-59	7	15
α-helix	63-64	2
β-strand	65-67	3	15
β-strand	70-73	4	13
β-strand	79-84	6	13
α-helix	87-89	3
β-strand	96-102	7	15
β-strand	107-113	7	15
α-helix	115-117	3
β-strand	119-120	2	14
α-helix	121-124	4
β-strand	125-130	6	16
β-strand	139-143	5	16
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-160	7	17
β-strand	170-174	5	17
β-strand	180-182	3	16
β-strand	191-200	10	17
α-helix	201	1
β-strand	207-208	2	14
β-strand	216-219	4	17

Chain G: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	29	1	9
β-strand	37	1	9
β-strand	39-44	6	8
β-strand	51-55	5	8
β-strand	66-67	2	8
α-helix	68	1
β-strand	76-83	6	7
β-strand	86-91	6	7
α-helix	96-98	3
β-strand	101-106	6	8
β-strand	117-118	2	8
β-strand	122-126	5	8
α-helix	127	1
β-strand	131	1	10
α-helix	132-133	2
β-strand	134-138	5	11
α-helix	139-141	3
α-helix	142-145	4
β-strand	149-159	11	11
β-strand	160	1	10
β-strand	165-170	6	12
β-strand	173-174	2	12
α-helix	175	1
β-strand	179-183	5	11
α-helix	184-187	4
β-strand	193-202	10	11
α-helix	203-207	5
β-strand	211-218	8	12
β-strand	221-228	8	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S1CE VARIANT OF FAB-EPR-1 heavy chain	A	protein	224	Homo sapiens
S1CE VARIANT OF FAB-EPR-1 light chain	G	protein	212	Homo sapiens
Erythropoietin receptor	D	protein	232	Homo sapiens	P19235 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VUI_1 S1CE VARIANT OF FAB-EPR-1 heavy chain (chains A)
EVQLVESGGGLVQPGGSLRLSCAASGFNLRSYYMHWVRQAPGKGLEWVASISPYYSYTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARHGYGAMDYWGQGTLVTVFNQIK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (G), FASTA

>8VUI_2 S1CE VARIANT OF FAB-EPR-1 light chain (chains G)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYSLITFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVSWYVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 3 (D), FASTA

>8VUI_3 Erythropoietin receptor (chains D)
APPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLE
DEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVL
LDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTE
CVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLDPHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (NH4, CL, NA, EDO) are not listed.

Primary citation

Antigen-binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones. Bruce, H.A., Singer, A.U., Blazer, L.L. et al. Protein Sci (2024) 33:e5081-e5081. DOI 10.1002/pro.5081 · 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
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…
4Y5Y 2.85 Å, Diabody 330 complex with EpoR
6MOF 2.89 Å, Monomeric DARPin G2 complex with EpoR

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