5YUA | pdb_00005yua

Crystal structure of voltage-gated sodium channel NavAb in high-pH condition

PDB DOI: https://doi.org/10.2210/pdb5YUA/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Aliarcobacter butzleri
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM

Deposited: 2017-11-21 Released: 2017-12-27
Deposition Author(s): Irie, K., Shimomura, T., Fujiyoshi, Y.
Funding Organization(s): Toyoaki Scholarship Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.262 (Depositor), 0.263 (DCC)
R-Value Work:
0.230 (Depositor), 0.231 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insight on the voltage dependence of prokaryotic voltage gated sodium channel NavAb.

Irie, K., Haga, Y., Shimomura, T., Fujiyoshi, Y.

(2017) FEBS Lett

PubMed: 29274127 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12955
Primary Citation Related Structures:
5YUA, 5YUB, 5YUC

PubMed Abstract:
Voltage-gated sodium channels are crucial for electro-signalling in living systems. Analysis of the molecular mechanism requires both fine electrophysiological evaluation and high-resolution channel structures. Here, we optimized a dual expression system of NavAb, which is a well-established standard of prokaryotic voltage-gated sodium channels, for E. coli and insect cells using a single plasmid vector to analyse high-resolution protein structures and measure large ionic currents. Using this expression system, we evaluated the voltage dependence and determined the crystal structures of NavAb wild-type and two mutants, E32Q and N49K, whose voltage dependence were positively shifted and essential interactions were lost in voltage sensor domain. The structural and functional comparison elucidated the molecular mechanisms of the voltage dependence of prokaryotic voltage-gated sodium channels.

Organizational Affiliation

Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Japan.

Macromolecule Content

Total Structure Weight: 37.15 kDa
Atom Count: 2,248
Modeled Residue Count: 228
Deposited Residue Count: 271
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein	A	271	Aliarcobacter butzleri	Mutation(s): 0 Gene Names: SAMEA4475700_01771 Membrane Entity: Yes
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018)) Explore A8EVM5 Go to UniProtKB: A8EVM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8EVM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX4 Query on PX4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
1N7 Query on 1N7 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHAPSO C₃₂ H₅₉ N₂ O₈ S GUQQBLRVXOUDTN-XOHPMCGNSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.262 (Depositor), 0.263 (DCC)
R-Value Work: 0.230 (Depositor), 0.231 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.45	α = 90
b = 126.45	β = 90
c = 201.658	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-27

Deposition Author(s):

Irie, K.

Shimomura, T.

Fujiyoshi, Y.

Funding Organization	Location	Grant Number
Toyoaki Scholarship Foundation	Japan	--

Revision History (Full details and data files)

Version 1.0: 2017-12-27
Type: Initial release
Version 1.1: 2018-01-17
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description