4V1D: Single chain antibody fragment lr, heavy chain

Ternary complex among two human derived single chain antibody fragments and Cn2 toxin from scorpion Centruroides noxius. Determined by X-ray diffraction at 3.1 Å resolution. Released 7 Oct 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: HOMO SAPIENS, CENTRUROIDES NOXIUS
Chains: 5
Atoms: 4,046
Mol. weight: 64.32 kDa
Released: 7 Oct 2015

Explore 4V1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V1D contains 14 α-helices and 59 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: 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

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	133-135	3
β-strand	136-139	4	3
β-strand	142-144	3	4
β-strand	151-157	7	3
β-strand	165-170	6	4
β-strand	176-181	6	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	231	1	3
β-strand	234-237	4	4

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	5
β-strand	6	1	6
β-strand	13	1	6
α-helix	14	1
β-strand	15	1	5
β-strand	20-21	2	5
α-helix	23-33	11
β-strand	38-42	5	5
β-strand	45-49	5	5
β-strand	55	1	7
α-helix	59-60	2

Chain D: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	65	1	8
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	106	1	7
β-strand	111-114	4	10
β-strand	115	1	8
β-strand	118-120	3	10
β-strand	121-122	2	9

Chain E: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	143	1	11
β-strand	144	1	12
β-strand	148-151	4	13
β-strand	157-162	6	12
β-strand	167-171	5	14
β-strand	173-178	6	13
β-strand	185-188	4	13
β-strand	202-207	6	12
β-strand	210-215	6	12
α-helix	220-222	3
β-strand	225-232	8	13
β-strand	237-240	4	13
β-strand	241	1	11
β-strand	244-248	5	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Single chain antibody fragment lr, heavy chain	A	protein	117	HOMO SAPIENS
Single chain antibody fragment lr, light chain	B	protein	146	HOMO SAPIENS
Beta-mammal toxin CN2	C	protein	66	CENTRUROIDES NOXIUS	P01495 (AlphaFold model)
Single chain antibody fragment RU1, heavy chain	D	protein	124	HOMO SAPIENS
Single chain antibody fragment RU1, light chain	E	protein	149	HOMO SAPIENS

Sequence of entity 1 (A), FASTA

>4V1D_1 SINGLE CHAIN ANTIBODY FRAGMENT LR, HEAVY CHAIN (chains A)
EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDY
ADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGFGSFDTWGQGTMVTVSS

Sequence of entity 2 (B), FASTA

>4V1D_2 SINGLE CHAIN ANTIBODY FRAGMENT LR, LIGHT CHAIN (chains B)
GGGGSGGGGSGGGGSEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPR
LLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVE
IKRAAAEQKLISEEDLNGAAHHHHHH

Sequence of entity 3 (C), FASTA

>4V1D_3 BETA-MAMMAL TOXIN CN2 (chains C)
KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPL
PNKRCS

Sequence of entity 4 (D), FASTA

>4V1D_4 SINGLE CHAIN ANTIBODY FRAGMENT RU1, HEAVY CHAIN (chains D)
QVNLRESGGGLVQPGGSLRLSCAASGFSFGSYGMHWVRQAPGKGLEWVAVISYGGGNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDARDCLLCADWHFDLWGRGTLV
TVSS

Sequence of entity 5 (E), FASTA

>4V1D_5 SINGLE CHAIN ANTIBODY FRAGMENT RU1, LIGHT CHAIN (chains E)
GGGGSGGGGSGGGGSNFMLTQPHSASGTPGQRVTISCSGSSSNIGSNTVNWYRHLPGSAP
ELLIGSHNQRPSGVPDRFSASKSDTSASLAISGLQSEDEADYYCAAWDDSLIGYVFGTGT
KLTVLGAAAEQKLISEEDLNGAAHHHHHH

Primary citation

Optimal Neutralization of Centruroides Noxius Venom is Understood Through a Structural Complex between Two Antibody Fragments and the Cn2 Toxin. Riano-Umbarila, L., Ledezma-Candanoza, L.M., Serrano-Posada, H. et al. J Biol Chem (2016) 291:1619. DOI 10.1074/JBC.M115.685297 · PubMed

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

2YC1 1.9 Å, Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in…
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
1CN2 Solution structure of toxin 2 from centruroides noxius hoffmann, a beta scorpion…

Browse structure collections

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