8VGM: Nav1.7

CryoEM structure of Nav1.7 in complex with engineered conformationally rigid Fab 7A9.4DS. Determined by electron microscopy at 2.6 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Aliarcobacter butzleri RM4018, Mus musculus
Chains: 8
Atoms: 15,626
Mol. weight: 236.67 kDa
Released: 30 Oct 2024

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

Secondary structure: helices and β-sheets

8VGM contains 94 α-helices and 82 β-strands across 8 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, B, C and D: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	1491-1501	11
α-helix	1504-1523	20
α-helix	1530-1558	29
α-helix	1559-1561	3
α-helix	1566-1583	18
α-helix	1585-1589	5
α-helix	1597-1600	4
α-helix	1603-1615	13
α-helix	1617-1655	39
α-helix	1660-1663	4
α-helix	1666-1677	12
α-helix	1682-1687	6
α-helix	1688-1691	4
α-helix	1695-1697	3
α-helix	1698-1755	58

Chains E and H: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	57-58	2	12
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	100E-103	4	12
β-strand	107-111	5	12
α-helix	115-116	2
α-helix	122-123	2
β-strand	124-128	5	13
α-helix	129-131	3
β-strand	140-149	10	13
β-strand	156-159	4	14
α-helix	160-162	3
β-strand	168-175	8	13
β-strand	180-188	9	13
α-helix	190-192	3
β-strand	199-204	6	14
α-helix	205-207	3
β-strand	209-214	6	14
α-helix	216-218	3

Chains F and L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	16
β-strand	19-28	11	15
α-helix	30-32	3
β-strand	33-38	6	16
β-strand	45-49	5	16
β-strand	53-54	2	16
α-helix	55	1
β-strand	62-75	14	15
α-helix	80-82	3
β-strand	85-92	8	16
β-strand	95-98	4	16
β-strand	102-106	5	16
α-helix	108-110	3
β-strand	111	1	17
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	18
β-strand	140	1	17
β-strand	144-145	2	19
β-strand	148-150	3	20
β-strand	153-154	2	20
α-helix	156-158	3
β-strand	159-163	5	18
β-strand	173-182	10	18
α-helix	183-187	5
β-strand	191-194	4	20
β-strand	197-198	2	19
β-strand	201	1	19
β-strand	207-210	4	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimeric Nav1.7-NavAb	A, B, C, D	protein	296	Aliarcobacter butzleri RM4018	A8EVM5 (AlphaFold model)
Fab 7A9.4DS heavy chain	E, H	protein	236	Mus musculus
Fab 7A9.4DS light chain	F, L	protein	215	Mus musculus

Sequence of entity 1 (A, B, C, D), FASTA

>8VGM_1 Chimeric Nav1.7-NavAb (chains A, B, C, D)
MDYKDDDDKGSLVPRGSHMYLRITNIVESSFFTKFIIYLIVLNMVTMMVEKEGQSQHMTE
VLYWINVVFIILFTIEIILRIYVHRISFFKDPWSLFDFVVVIISIVGMFLADLIETYFVS
PTLFRVIRLARIGRILRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQL
FGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMIN
LVVAIIVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Sequence of entity 2 (E, H), FASTA

>8VGM_2 Fab 7A9.4DS heavy chain (chains E, H)
EVQLVESGGGCVKPGGSLKLSCAASGFTFSNYAMSWVRQTPEKRLEWVATISNGGRYTYY
PDSVKGRFTISRDNAKNSLYLQMSSLRSEDTAMYYCARHLYRYDVGGALDYWGQGTCVTV
SSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFCECPVTLTWNSGSLSSGVHTFPAVL
QSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPHHHHHHP

Sequence of entity 3 (F, L), FASTA

>8VGM_3 Fab 7A9.4DS light chain (chains F, L)
EIVLTQSPALMAASPGEKVTITCSVSLSISSSNLFWYQQKCETSPKPWIYGTSKLASGVP
VRFSGSGSGTSYSLTISSMECEDAATYYCQQWSSHSFTFGGGTKLEIKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTCQDSKDCTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM. Kung, J.E., Johnson, M.C., Jao, C.C. et al. bioRxiv (2024). DOI 10.1101/2024.05.10.593593 · PubMed

Other PDB entries of the same protein (UniProt A8EVM5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MWD 2.33 Å, NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206S
6MWA 2.4 Å, NavAb Voltage-gated Sodium Channel, residues 1-239
9UC1 2.5 Å, Crystal structure of voltage-gated sodium channel NavAb N49K/S178T mutant
6MWG 2.5 Å, NavAb Voltage-gated Sodium Channel, residues 1-239, with mutation T206V
6C1M 2.52 Å, NavAb NormoPP mutant
8DIV 2.54 Å, Crystal structure of NavAb I22V as a basis for the human Nav1.7 Inherited…
6MWB 2.6 Å, NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206A
8VGL 2.6 Å, CryoEM structure of Nav1.7 in complex with wild type Fab 7A9
3RVY 2.7 Å, Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.7 A)
5KLB 2.7 Å, Crystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A)
6C1K 2.7 Å, HypoPP mutant with ligand1
8DJ0 2.7 Å, Crystal structure of NavAb L123T as a basis for the human Nav1.7 Inherited…

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