5YUA: Ion transport protein

Crystal structure of voltage-gated sodium channel NavAb in high-pH condition. Determined by X-ray diffraction at 2.8 Å resolution. Released 27 Dec 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Arcobacter butzleri
Chains: 1
Atoms: 2,248
Mol. weight: 37.15 kDa
Ligands: PX4, 1N7, LMT, CA
Released: 27 Dec 2017

Explore 5YUA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YUA contains 17 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: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	1001-1009	9
α-helix	1012-1031	20
α-helix	1035-1067	33
α-helix	1069-1072	4
α-helix	1075-1088	14
α-helix	1090	1
α-helix	1098-1101	4
α-helix	1102-1107	6
α-helix	1108-1112	5
α-helix	1114-1126	13
α-helix	1127-1130	4
α-helix	1131-1152	22
α-helix	1157-1160	4
α-helix	1163-1174	12
α-helix	1179-1184	6
α-helix	1185-1188	4
α-helix	1195-1224	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ion transport protein	A	protein	271	Arcobacter butzleri	A8EVM5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YUA_1 Ion transport protein (chains A)
GSGSMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIF
TIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQM
RKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTL
ESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAIIVDAMAILNQKEEQHIIDEV
QSHEDNINNEIIKLREEIVELKELIKTSLKN

Ligands and cofactors

ID	Name	Formula	Copies
PX4	1,2-dimyristoyl-sn-glycero-3-phosphocholine	C36 H73 N O8 P	6
1N7	Chapso	C32 H59 N2 O8 S	1
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	2
CA	Calcium ion	Ca	1

Primary citation

Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb. Irie, K., Haga, Y., Shimomura, T. et al. FEBS Lett (2017). DOI 10.1002/1873-3468.12955 · 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

Browse structure collections

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