8VVM: FabS1CE1-EPR1-1

Structure of FabS1CE1-EPR1-1 in complex with the erythropoietin receptor. Determined by X-ray diffraction at 2.9 Å resolution. Released 10 Jul 2024.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,951
Mol. weight: 120.65 kDa
Released: 10 Jul 2024

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

Secondary structure: helices and β-sheets

8VVM contains 40 α-helices and 102 β-strands across 5 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-13	3	2
β-strand	19-26	8	1
α-helix	30-36	3
β-strand	39-44	6	2
β-strand	50-56	7	2
β-strand	65-67	3	2
β-strand	76-81	6	1
α-helix	82-84	3
β-strand	86-91	6	1
α-helix	96-98	3
β-strand	100-108	9	2
β-strand	114-118	5	2
β-strand	122-126	5	2
β-strand	131	1	3
β-strand	134-138	5	4
α-helix	139-141	3
β-strand	149-159	11	4
β-strand	160	1	3
β-strand	165-168	4	5
α-helix	169-171	3
β-strand	173	1	5
β-strand	177-179	3	4
α-helix	180-182	3
β-strand	183-184	2	4
β-strand	190-199	10	4
α-helix	200-202	3
β-strand	208-214	7	5
α-helix	215-217	3
β-strand	219-225	7	5

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	11
β-strand	18-24	7	12
β-strand	39-44	6	11
β-strand	50-57	8	11
β-strand	64-67	4	11
β-strand	76-81	6	12
α-helix	82-84	3
β-strand	86-92	7	12
α-helix	96-98	3
β-strand	100-104	5	11
β-strand	122-126	5	11
β-strand	131	1	13
β-strand	134-138	5	14
α-helix	139-141	3
β-strand	149-159	11	14
β-strand	160	1	13
β-strand	165-168	4	15
α-helix	169-171	3
β-strand	173	1	15
β-strand	177-179	3	14
α-helix	180-182	3
β-strand	183-184	2	14
β-strand	190-199	10	14
α-helix	200-202	3
β-strand	208-214	7	15
α-helix	215-217	3
β-strand	219-225	7	15

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	39-44	6	17
β-strand	51-55	5	17
β-strand	66-67	2	17
α-helix	68	1
β-strand	76-83	6	16
β-strand	86-91	6	16
α-helix	96-98	3
β-strand	101-107	7	17
β-strand	116-118	3	17
β-strand	122-126	5	17
β-strand	131	1	18
α-helix	132-133	2
β-strand	134-138	5	19
α-helix	139-141	3
α-helix	142-146	5
β-strand	149-159	11	19
β-strand	160	1	18
β-strand	165-170	6	20
β-strand	173-174	2	20
α-helix	175	1
β-strand	179-183	5	19
α-helix	184-187	4
β-strand	193-202	10	19
α-helix	203-207	5
β-strand	211-218	8	20
β-strand	221-228	8	20

Chain G: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	39-44	6	7
β-strand	51-55	5	7
β-strand	66-67	2	7
α-helix	68	1
β-strand	76-83	6	6
β-strand	86-91	6	6
α-helix	96-98	3
β-strand	101-107	7	7
β-strand	116-118	3	7
β-strand	122-126	5	7
β-strand	131	1	8
α-helix	132-133	2
β-strand	134-138	5	9
α-helix	139-141	3
α-helix	142-145	4
β-strand	149-159	11	9
β-strand	160	1	8
β-strand	165-170	6	10
β-strand	173-174	2	10
β-strand	179-183	5	9
α-helix	184-187	4
β-strand	193-202	10	9
α-helix	203-207	5
β-strand	211-218	8	10
β-strand	221-228	8	10

Chain I: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
α-helix	19-21	3
β-strand	27-29	3	21
β-strand	30	1	22
β-strand	37-41	5	21
β-strand	53-59	7	23
α-helix	63-64	2
β-strand	65-66	2	23
α-helix	67-69	3
β-strand	70-73	4	21
β-strand	79-84	6	21
α-helix	87-90	4
β-strand	96-102	7	23
β-strand	107-113	7	23
α-helix	115-117	3
β-strand	119-120	2	22
α-helix	121-124	4
β-strand	125-130	6	24
β-strand	139-143	5	24
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-161	8	25
β-strand	169-174	6	25
β-strand	180-181	2	24
β-strand	191-200	10	25
β-strand	207-208	2	22
α-helix	209-215	7
β-strand	216-219	4	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S1CE1 VARIANT OF FAB-EPR-1 heavy chain	A, B	protein	224	Homo sapiens
S1CE1 VARIANT OF FAB-EPR-1 light chain	C, G	protein	212	Homo sapiens
Erythropoietin receptor	I	protein	232	Homo sapiens	P19235 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8VVM_1 S1CE1 VARIANT OF FAB-EPR-1 heavy chain (chains A, B)
EVQLVESGGGLVQPGGSLRLSCAASGFNLRSYYMHWVRQAPGKGLEWVASISPYYSYTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARHGYGAMDYWGQGTLVTVFNQIK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPGPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (C, G), FASTA

>8VVM_2 S1CE1 VARIANT OF FAB-EPR-1 light chain (chains C, G)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYSLITFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVSWYVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 3 (I), FASTA

>8VVM_3 Erythropoietin receptor (chains I)
APPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLE
DEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVL
LDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTE
CVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLDPHHHHHH

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
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…
4Y5Y 2.85 Å, Diabody 330 complex with EpoR

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