8DJ0: Ion transport protein

Crystal structure of NavAb L123T as a basis for the human Nav1.7 Inherited Erythromelalgia I848T mutation. Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Apr 2023.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Aliarcobacter butzleri RM4018
Chains: 1
Atoms: 2,207
Mol. weight: 34.4 kDa
Ligands: CPS, PX4
Released: 12 Apr 2023

Explore 8DJ0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DJ0 contains 16 α-helices and 0 β-strands across 1 chain. 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: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	1001-1009	9
α-helix	1012-1031	20
α-helix	1035-1067	33
α-helix	1068-1071	4
α-helix	1075-1086	12
α-helix	1096-1101	6
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1114-1125	12
α-helix	1127-1152	26
α-helix	1157-1160	4
α-helix	1163-1175	13
α-helix	1179-1184	6
α-helix	1185-1188	4
α-helix	1192-1194	3
α-helix	1195-1237	43

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ion transport protein	A	protein	257	Aliarcobacter butzleri RM4018	A8EVM5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8DJ0_1 Ion transport protein (chains A)
MDYKDDDDKGSLVPRGSHMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFG
VYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLR
VLRLFRLVTAVPQMRKIVSATISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGT
LGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMA
ILNQKEEQHIIDEVQSH

Ligands and cofactors

ID	Name	Formula	Copies
CPS	3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate	C32 H58 N2 O7 S	2
PX4	1,2-dimyristoyl-sn-glycero-3-phosphocholine	C36 H73 N O8 P	5

Primary citation

Structural basis for severe pain caused by mutations in the S4-S5 linkers of voltage-gated sodium channel Na V 1.7. Wisedchaisri, G., Gamal El-Din, T.M., Zheng, N. et al. Proc Natl Acad Sci U S A (2023) 120:e2219624120-e2219624120. DOI 10.1073/pnas.2219624120 · 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
8VGM 2.6 Å, CryoEM structure of Nav1.7 in complex with engineered conformationally rigid Fab 7A9.4DS
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

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