2YC1: Single chain antibody fragment 9004G

Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann. Determined by X-ray diffraction at 1.9 Å resolution. Released 13 Apr 2011.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: HOMO SAPIENS, CENTRUROIDES NOXIUS HOFFMANN
Chains: 6
Atoms: 5,154
Mol. weight: 71.95 kDa
Released: 13 Apr 2011

Explore 2YC1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YC1 contains 24 α-helices and 58 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.

Chains A and D: 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
α-helix	53-55	3
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	92-101	10	2
β-strand	103-107	5	2
β-strand	111-115	5	2

Chains B and E: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	133-135	3
β-strand	136-139	4	3
β-strand	142-145	4	4
β-strand	151-157	7	3
β-strand	165-170	6	4
β-strand	177-181	5	4
β-strand	185-186	2	4
α-helix	187	1
β-strand	194-199	6	3
β-strand	202-207	6	3
α-helix	212-214	3
β-strand	217-222	6	4
α-helix	228	1
β-strand	229-230	2	4
β-strand	234-238	5	4

Chains C and F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	5
β-strand	6	1	6
α-helix	12	1
β-strand	13	1	6
α-helix	14	1
β-strand	15	1	5
β-strand	20	1	5
α-helix	23-33	11
β-strand	38-42	5	5
β-strand	45-49	5	5
α-helix	60	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Single chain antibody fragment 9004G	A, D	protein	117	HOMO SAPIENS
Single chain antibody fragment 9004G	B, E	protein	146	HOMO SAPIENS
Beta-mammal toxin CN2	C, F	protein	66	CENTRUROIDES NOXIUS HOFFMANN	P01495 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>2YC1_1 SINGLE CHAIN ANTIBODY FRAGMENT 9004G (chains A, D)
EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDY
ADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTVSS

Sequence of entity 2 (B, E), FASTA

>2YC1_2 SINGLE CHAIN ANTIBODY FRAGMENT 9004G (chains B, E)
GGGGSGGGGSGGGGSEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPR
LLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVE
IKRAAAEQKLISEEDLNGAAHHHHHH

Sequence of entity 3 (C, F), FASTA

>2YC1_3 BETA-MAMMAL TOXIN CN2 (chains C, F)
KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPL
PNKRCS

Primary citation

Structural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides Noxius Hoffmann by a Human-Derived Single Chain Antibody Fragment. Canul-Tec, J.C., Riano-Umbarila, L., Rudino-Pinera, E. et al. J Biol Chem (2011) 286:20892. DOI 10.1074/JBC.M111.238410 · PubMed

Other PDB entries of the same protein (UniProt P01495 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2YBR 2.55 Å, Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in…
25IH 2.8 Å, Cryo-EM structure of human Nav1.6 in complex with Cn2
4V1D 3.1 Å, Ternary complex among two human derived single chain antibody fragments and Cn2 toxin…
1CN2 Solution structure of toxin 2 from centruroides noxius hoffmann, a beta scorpion…

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