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- PDB-3b8e: Crystal structure of the sodium-potassium pump -

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Basic information

Entry
Database: PDB / ID: 3b8e
TitleCrystal structure of the sodium-potassium pump
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • Na+/K+ ATPase gamma subunit transcript variant a
KeywordsHYDROLASE/TRANSPORT PROTEIN / Na+ / K+-ATPASE / P-TYPE ATPASE / CATION PUMP / MEMBRANE PROTEIN / HYDROLASE / ATP-BINDING / CALCIUM TRANSPORT / ION TRANSPORT / MEMBRANE POTENTIAL / PHOSPHORYLATION / Magnesium / Metal-binding / Nucleotide-binding / Potassium / Potassium transport / Sodium / Sodium transport / Sodium/potassium transport / Transmembrane / Glycoprotein / Signal-anchor / HYDROLASE-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


Ion homeostasis / Ion transport by P-type ATPases / regulation of monoatomic ion transport / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / regulation of calcium ion transmembrane transport ...Ion homeostasis / Ion transport by P-type ATPases / regulation of monoatomic ion transport / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / regulation of calcium ion transmembrane transport / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / ion channel regulator activity / positive regulation of potassium ion transmembrane transport / intracellular sodium ion homeostasis / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of sodium ion transmembrane transport / regulation of sodium ion transport / ATPase activator activity / potassium ion binding / organelle membrane / intracellular potassium ion homeostasis / potassium ion import across plasma membrane / intercalated disc / lateral plasma membrane / transporter activator activity / sperm flagellum / ATP metabolic process / cardiac muscle contraction / proton transmembrane transport / T-tubule / protein localization to plasma membrane / sarcolemma / intracellular calcium ion homeostasis / transmembrane transport / melanosome / regulation of gene expression / ATPase binding / basolateral plasma membrane / protein-macromolecule adaptor activity / cell adhesion / protein stabilization / apical plasma membrane / innate immune response / axon / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Calcium-transporting ATPase, cytoplasmic domain N ...: / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Sodium and potassium ATPases beta subunits signature 2. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / : / P-type ATPase subfamily IIC, subunit alpha / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / HAD superfamily/HAD-like / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROMAGNESATE(2-) / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / RUBIDIUM ION / Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-1 / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 Å
AuthorsMorth, J.P. / Pedersen, P.B. / Toustrup-Jensen, M.S. / Soerensen, T.L.M. / Petersen, J. / Andersen, J.P. / Vilsen, B. / Nissen, P.
CitationJournal: Nature / Year: 2007
Title: Crystal structure of the sodium-potassium pump.
Authors: Morth, J.P. / Pedersen, B.P. / Toustrup-Jensen, M.S. / Sorensen, T.L. / Petersen, J. / Andersen, J.P. / Vilsen, B. / Nissen, P.
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: Na+/K+ ATPase gamma subunit transcript variant a
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
H: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,87818
Polymers237,5366
Non-polymers2,34212
Water00
1
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9399
Polymers118,7683
Non-polymers1,1716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
MethodPISA
2
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
H: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9399
Polymers118,7683
Non-polymers1,1716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.930, 261.500, 334.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Sodium/potassium-transporting ATPase subunit ... , 2 types, 4 molecules ACBD

#1: Protein Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium pump subunit alpha-1 / Na+ / /K+ / ATPase alpha-1 subunit


Mass: 110320.734 Da / Num. of mol.: 2 / Fragment: residues 19-1016 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: Kidney / References: UniProt: P05024, EC: 3.6.3.9
#2: Protein/peptide Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase beta-1 subunit / Sodium Pump


Mass: 5225.194 Da / Num. of mol.: 2 / Fragment: residues 28-73 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: Kidney / References: UniProt: P05027

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Protein/peptide , 1 types, 2 molecules GH

#3: Protein/peptide Na+/K+ ATPase gamma subunit transcript variant a


Mass: 3221.925 Da / Num. of mol.: 2 / Fragment: residues 23-51 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: Kidney / References: UniProt: Q58K79

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Non-polymers , 4 types, 12 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Rb
#6: Chemical ChemComp-MF4 / TETRAFLUOROMAGNESATE(2-) / MAGNESIUMTETRAFLUORIDE


Mass: 100.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F4Mg
#7: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM

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Details

Has protein modificationY
Nonpolymer detailsTHE AUTHORS ONLY SEE DENSITY FOR THE PHOSPHATIDYLCHOLINE LIPID HEAD GROUP AND THEY DO NOT HAVE ANY ...THE AUTHORS ONLY SEE DENSITY FOR THE PHOSPHATIDYLCHOLINE LIPID HEAD GROUP AND THEY DO NOT HAVE ANY EXPERIMENTAL EVIDENCE FOR PC1.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.35 Å3/Da / Density % sol: 80.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 2000mme, 0.2M Choline Chloride, 4% Glycerol, 4% MPD, 0.04M DTT, 0.1-04% beta-DDM, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.078, 1.073, 0.81
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0781
21.0731
30.811
ReflectionResolution: 3.5→48 Å / Num. all: 77565 / Num. obs: 77431 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.8 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.258 / Rsym value: 0.258 / Net I/σ(I): 11.24
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 14 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 2.56 / Num. unique all: 6208 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.5→20 Å / Isotropic thermal model: GROUPED B-factors / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3129 1541 -RANDOM
Rwork0.2774 ---
all-77267 --
obs-76989 99.6 %-
Displacement parametersBiso mean: 104 Å2
Baniso -1Baniso -2Baniso -3
1-3.508 Å20 Å20 Å2
2--17.739 Å20 Å2
3----21.247 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å1.15 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16676 0 42 0 16718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008002
X-RAY DIFFRACTIONc_angle_deg1.51826
X-RAY DIFFRACTIONc_improper_angle_d1.086
X-RAY DIFFRACTIONc_dihedral_angle_d22.642
Refine LS restraints NCSNCS model details: RESTRAINED NCS ON DOMAINS: A(resid 19:80 and 154:274 and 344:382 and 592:765), A(383:591), A(91:153), A(275:343 and 2003:2005), A(766:1016 and B and G)
Rms dev Biso : 3 Å2 / Weight position: 500
LS refinement shellResolution: 3.5→3.54 Å
RfactorNum. reflection
Rfree0.385 39
Rwork0.4291 -
obs-2279

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