8YHZ: Light chain of 1080 Fab

The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide. Determined by X-ray diffraction at 1.62 Å resolution. Released 23 Oct 2024.

Method: X-ray diffraction
Resolution: 1.62 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 3
Atoms: 3,816
Mol. weight: 47.41 kDa
Released: 23 Oct 2024

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

Secondary structure: helices and β-sheets

8YHZ contains 23 α-helices and 43 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 H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	10-11	2	7
β-strand	17-24	8	6
α-helix	28-30	3
β-strand	33-38	6	8
β-strand	44-50	7	8
β-strand	56-58	3	8
α-helix	60-62	3
β-strand	66-70	5	6
β-strand	74-79	6	6
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	101-102	2	8
β-strand	106-108	3	8
β-strand	109-110	2	7
α-helix	114-115	2
β-strand	116	1	9
α-helix	117-118	2
β-strand	119-123	5	10
α-helix	124-126	3
β-strand	134-144	11	10
β-strand	145	1	9
β-strand	150-153	4	11
α-helix	154-156	3
β-strand	162-164	3	10
α-helix	165-167	3
β-strand	168-169	2	10
β-strand	175-184	10	10
α-helix	185-187	3
β-strand	193-199	7	11
α-helix	200-202	3
β-strand	204-210	7	11

Chain L: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6	1
α-helix	8	1
β-strand	9-12	4	2
β-strand	17-23	7	1
α-helix	26-27	2
α-helix	28-30	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-91	8	2
β-strand	100-102	3	2
β-strand	106-111	6	2
β-strand	115	1	3
α-helix	116-117	2
β-strand	118-122	5	4
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	4
β-strand	144	1	3
β-strand	149-154	6	5
β-strand	157-158	2	5
α-helix	159	1
β-strand	163-167	5	4
α-helix	168-171	4
β-strand	177-186	10	4
α-helix	187-190	4
β-strand	195-201	7	5
β-strand	209-214	6	5

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	213-217	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain of 1080 Fab	L	protein	218	Oryctolagus cuniculus
Heavy chain of 1080 Fab	H	protein	214	Oryctolagus cuniculus
Sodium channel protein type 9 subunit alpha	P	protein	11	Homo sapiens	Q15858 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8YHZ_1 Light chain of 1080 Fab (chains L)
QVLTQTASPVSAAVGNTVTITCQSSQSVWKNNDLSWYQQKLGQPPKLLIYYASTLASGVS
SRFKASGSGTQFTLTISDVQCDDAGTYYCVGSYDCSSADCNAFGGGTKVVVKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 2 (H), FASTA

>8YHZ_2 Heavy chain of 1080 Fab (chains H)
QSEEESGGRLVTPETPLTLTCTASGIDLSKWPMTWVRQAPGKGLEWIGIIGRSGSTNYAS
WAKGRFTISKTSTTVDLKMTSPTTEDTATYFCARGGSYYDLWGQGTLVTVSSASTKGPSV
FPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSV
VTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 3 (P), FASTA

>8YHZ_3 Sodium channel protein type 9 subunit alpha (chains P)
EHHPMTEEFKN

Primary citation

Intra-channel bi-epitopic crosslinking unleashes ultrapotent antibodies targeting Na V 1.7 for pain alleviation. Zhang, Y., Ding, Y., Zeng, Z. et al. Cell Rep Med (2024) 5:101800-101800. DOI 10.1016/j.xcrm.2024.101800 · PubMed

Other PDB entries of the same protein (UniProt Q15858 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9Y7F 1.7 Å, Crystal structure of nanobody R3D8 in complex with human voltage-gated sodium channel…
7W9K 2.2 Å, Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution
8F0P 2.2 Å, Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-1305
8F0Q 2.5 Å, Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the acylsulfonamide inhibitor…
8I5Y 2.6 Å, Structure of human Nav1.7 in complex with vixotrigine
21TQ 2.7 Å, The structure of Nav1.7 with veratridine standing near the IFM motif (site I)
7XVE 2.7 Å, Human Nav1.7 mutant class-I
8I5B 2.7 Å, Structure of human Nav1.7 in complex with bupivacaine
8I5G 2.7 Å, Structure of human Nav1.7 in complex with PF-05089771
8THH 2.7 Å, Cryo-EM structure of Nav1.7 with LTG
7XVF 2.8 Å, Nav1.7 mutant class2
8G1A 2.8 Å, Cryo-EM structure of Nav1.7 with CBD

Browse structure collections

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