3WGV

Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state with oligomycin

• PDB DOI: https://doi.org/10.2210/pdb3WGV/pdb

• Classification: HYDROLASE/TRANSPORT PROTEIN/ANTIBIOTIC
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2013-08-09 Released: 2013-10-09 
• Deposition Author(s): Kanai, R., Ogawa, H., Vilsen, B., Cornelius, F., Toyoshima, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.298 
• R-Value Work: 0.270 
• R-Value Observed: 0.270 

Literature

Crystal structure of a Na1-bound Na1,K1-ATPase preceding the E1P state

Kanai, R., Ogawa, H., Vilsen, B., Cornelius, F., Toyoshima, C.

(2013) Nature 502: 201-206

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 322.98 kDa 
• Atom Count: 21,909 
• Modelled Residue Count: 2,663 
• Deposited Residue Count: 2,768 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit alpha-1	A, D [auth C]	1,016	Sus scrofa	Mutation(s): 0  EC: 3.6.3.9
UniProt
Find proteins for P05024 (Sus scrofa) Go to UniProtKB:  P05024

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit beta-1	B, E [auth D]	303	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P05027 (Sus scrofa) Go to UniProtKB:  P05027

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Na+/K+ ATPase gamma subunit transcript variant a	C [auth G], F [auth E]	65	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for Q58K79 (Sus scrofa) Go to UniProtKB:  Q58K79

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EFO	KA [auth C], U [auth A]	Oligomycin A C45 H74 O11 MNULEGDCPYONBU-AWJDAWNUSA-N
PC1	GA [auth C], HA [auth C], IA [auth C], JA [auth C], NA [auth D], Q [auth A], R [auth A], S [auth A], T [auth A], V [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N
ADP	BA [auth C], J [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CLR	LA [auth D], MA [auth D], O [auth A], P [auth A], PA [auth E], X [auth G]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	OA [auth D], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ALF	H [auth A], Z [auth C]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG	AA [auth C], G [auth A], I [auth A], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	CA [auth C], DA [auth C], EA [auth C], FA [auth C], K [auth A], L [auth A], M [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.298 
• R-Value Work: 0.270 
• R-Value Observed: 0.270 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.285	α = 90
b = 210.183	β = 90
c = 256.086	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Kanai, R., Ogawa, H., Vilsen, B., Cornelius, F., Toyoshima, C.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary