9Y7F: Nanobody R3D8

Crystal structure of nanobody R3D8 in complex with human voltage-gated sodium channel Nav1.7 P-loop 1. Determined by X-ray diffraction at 1.7 Å resolution. Released 16 Sept 2026.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Vicugna pacos, Homo sapiens
Chains: 2
Atoms: 1,287
Mol. weight: 17.88 kDa
Released: 16 Sept 2026

Explore 9Y7F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y7F contains 3 α-helices and 11 β-strands across 2 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: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-13	4	2
β-strand	18-25	8	1
β-strand	32-39	8	2
β-strand	46-52	7	2
β-strand	58-60	3	2
β-strand	68-72	5	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-102	11	2
β-strand	106-111	6	2
β-strand	115-120	6	2

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	286-290	5
α-helix	296-303	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody R3D8	A	protein	127	Vicugna pacos
Sodium channel protein type 9 subunit alpha	B	protein	31	Homo sapiens	Q15858 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9Y7F_1 Nanobody R3D8 (chains A)
QVQLQESGGGLVQDGGSLRLSCVASGFIFDDYAIGWFRQAPGKEREFVAAISWNGLSTRY
ADSVKGRFTISRDNAKIAVYLQMDNLTPDDTARYYCTMRAWSENTGNFASRGQGTQVTVS
SHHHHHH

Sequence of entity 2 (B), FASTA

>9Y7F_2 Sodium channel protein type 9 subunit alpha (chains B)
CFRNSLENNETLESIMNTLESEEDFRKYFCS

Primary citation

Antigen-Detected NMR for Minimal Epitope Engineering and Structure-Guided Selection of a Na V 1.7-Selective Nanobody. Liu, J., Chen, W., Cristofori-Armstrong, B. et al. Adv Sci (Weinh) (2026):e77611-e77611. DOI 10.1002/advs.77611 · PubMed

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

8YHZ 1.62 Å, The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide
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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