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

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Basic information

Entry
Database: PDB / ID: 3kdp
TitleCrystal structure of the sodium-potassium pump
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • Na+/K+ ATPase gamma subunit transcript variant a
KeywordsHYDROLASE / alpha helical / heterotrimeric membrane protein complex / ATP-binding / Ion transport / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Potassium / Potassium transport / Sodium transport / Sodium/potassium transport / Transmembrane / Transport / Disulfide bond / Glycoprotein / Signal-anchor
Function / homology
Function and homology information


Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex ...Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / regulation of calcium ion transmembrane transport / intracellular potassium ion homeostasis / establishment or maintenance of transmembrane electrochemical gradient / intracellular sodium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / ion channel regulator activity / relaxation of cardiac muscle / potassium ion import across plasma membrane / ATPase activator activity / potassium ion binding / organelle membrane / intercalated disc / lateral plasma membrane / sperm flagellum / ATP metabolic process / regulation of sodium ion transport / cardiac muscle contraction / T-tubule / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / transmembrane transport / intracellular calcium ion homeostasis / melanosome / protein-macromolecule adaptor activity / ATPase binding / regulation of gene expression / basolateral plasma membrane / protein stabilization / cell adhesion / apical plasma membrane / axon / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Na, k-atpase alpha subunit. / : / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A ...Na, k-atpase alpha subunit. / : / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / 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. / Sodium and potassium ATPases beta subunits signature 2. / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Distorted Sandwich / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CHOLESTEROL / TETRAFLUOROMAGNESATE(2-) / 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, B.P. / 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
DepositionOct 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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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)294,29018
Polymers292,7546
Non-polymers1,53512
Water0
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)147,1459
Polymers146,3773
Non-polymers7686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-78 kcal/mol
Surface area58660 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)147,1459
Polymers146,3773
Non-polymers7686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-77 kcal/mol
Surface area58610 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 19:80 or resseq 154:274 or resseq...
211chain C and (resseq 19:80 or resseq 154:274 or resseq...
112chain A and (resseq 383:591 )
212chain C and (resseq 383:591 )
113chain A and (resseq 766:1016 )
213chain C and (resseq 766:1016 )
114chain B and (resseq 18:303 )
214chain D and (resseq 18:303 )
115chain G and (resseq 23:49 )
215chain H and (resseq 23:49 )

NCS ensembles :
ID
1
2
3
4
5

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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: ALPHA chain (UNP RESIDUES 24-1021) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: medula / References: UniProt: P05024, EC: 3.6.3.9
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 33104.902 Da / Num. of mol.: 2 / Fragment: BETA chain (UNP RESIDUES 18-303) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: medula / 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: 2951.573 Da / Num. of mol.: 2 / Fragment: GAMMA chain (UNP RESIDUES 23-49) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: medula / References: UniProt: Q58K79

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Non-polymers , 4 types, 12 molecules

#4: Chemical ChemComp-MF4 / TETRAFLUOROMAGNESATE(2-) / MAGNESIUMTETRAFLUORIDE


Mass: 100.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F4Mg
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 85.468 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Rb
#7: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O

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Details

Sequence detailsFOR THE CHAIN B AND D, THE EXPERIMENTAL INFO OF UNIPROT (P05027, AT1B1_PIG) SHOWS CONFLICT AT THIS ...FOR THE CHAIN B AND D, THE EXPERIMENTAL INFO OF UNIPROT (P05027, AT1B1_PIG) SHOWS CONFLICT AT THIS POSITION: F -> S (IN REF. 1: CAA27575)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.15 Å3/Da / Density % sol: 76.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 14% PEG 2000 MME, 0.2M CHOLINE CHLORIDE, 4% GLYCEROL, 4% MPD, 0.04M DTT, 0.1-04% BETA-DDM, pH 7.0, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 3.5→48 Å / Num. obs: 77431 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.8 % / Rmerge(I) obs: 0.258 / Rsym value: 0.258 / Net I/σ(I): 13.8
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 2.56

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Processing

Software
NameVersionClassification
RemDAqdata collection
SHARPphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
XDSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.5→38.858 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 1550 2 %Random
Rwork0.2422 ---
obs0.2431 77402 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.413 Å2 / ksol: 0.254 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7422 Å20 Å20 Å2
2--14.918 Å20 Å2
3----22.6603 Å2
Refinement stepCycle: LAST / Resolution: 3.5→38.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20556 0 74 0 20630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121054
X-RAY DIFFRACTIONf_angle_d1.43328534
X-RAY DIFFRACTIONf_dihedral_angle_d21.7287858
X-RAY DIFFRACTIONf_chiral_restr0.0893214
X-RAY DIFFRACTIONf_plane_restr0.0073666
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2952X-RAY DIFFRACTIONPOSITIONAL
12C2952X-RAY DIFFRACTIONPOSITIONAL0.058
21A1643X-RAY DIFFRACTIONPOSITIONAL
22C1643X-RAY DIFFRACTIONPOSITIONAL0.045
31A2046X-RAY DIFFRACTIONPOSITIONAL
32C2046X-RAY DIFFRACTIONPOSITIONAL0.037
41B2330X-RAY DIFFRACTIONPOSITIONAL
42D2330X-RAY DIFFRACTIONPOSITIONAL0.025
51G208X-RAY DIFFRACTIONPOSITIONAL
52H208X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5003-3.61320.35031330.33436653X-RAY DIFFRACTION97
3.6132-3.74220.33881500.30586774X-RAY DIFFRACTION100
3.7422-3.89190.3181490.2916815X-RAY DIFFRACTION100
3.8919-4.06890.28981240.26016875X-RAY DIFFRACTION100
4.0689-4.28310.27121480.22676837X-RAY DIFFRACTION100
4.2831-4.55110.25011330.19846837X-RAY DIFFRACTION100
4.5511-4.90190.23331550.17886871X-RAY DIFFRACTION100
4.9019-5.3940.22541250.17956915X-RAY DIFFRACTION100
5.394-6.17190.261410.19966948X-RAY DIFFRACTION100
6.1719-7.76570.27921520.20777024X-RAY DIFFRACTION100
7.7657-38.860.26581400.22817303X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4106-0.7014-0.50532.480.98982.8283-0.1281-0.6707-0.20130.3261-0.0402-0.04640.4478-0.08640.34170.02870.0662-0.05680.1054-0.28580.6201-17.2876-24.130429.2308
23.83992.45741.45763.86433.16094.6369-0.83320.12350.3515-0.2737-0.13981.1119-0.3677-0.14830.89950.4839-0.0386-0.01720.4616-0.39190.8634-46.4385-27.33668.3618
32.0382.26161.49815.44230.43653.48670.7905-0.55560.23571.706-0.08360.13610.9152-1.47-0.14641.39570.38120.00861.0598-0.32980.7504-11.6078-24.146473.8578
41.8057-0.3397-0.77510.08760.1030.4128-0.1498-0.65190.18020.22880.1531-0.06870.00770.4015-1.29860.63320.60390.40470.3731-0.51160.9136-12.5838-10.208173.9284
50.1918-0.45590.16411.7731.13514.4999-0.227-0.0087-0.0078-0.2001-0.26510.2230.5612-1.00940.50590.33490.05430.24751.3343-0.69650.9303-26.0454-3.650881.0545
61.2298-0.26090.08892.397-1.47683.512-0.0765-0.46170.00290.110.0150.3497-0.5414-0.20870.04740.17610.1142-0.1140.31710.05610.5678-11.856-89.742234.817
74.33230.45950.57932.1569-2.61985.6845-0.38620.1506-0.49970.07480.0075-0.48040.04140.05860.34730.3729-0.12510.03240.1023-0.04540.557718.4375-91.131915.0653
82.41351.7639-2.38563.90930.27443.9277-0.4295-1.1121-0.03961.03210.2297-0.2624-0.50781.4009-0.1981.26160.44860.12791.352-0.01740.831-19.1852-86.028179.1043
91.155-1.5001-0.17142.02070.02773.55440.0258-0.8246-0.37210.1514-0.02730.5969-0.3059-0.0730.0580.59880.0542-0.16331.09220.23320.7188-19.5701-99.955880.316
101.4983-1.1287-1.19191.5171-0.50963.6616-0.332-0.13190.1239-0.1189-0.03510.049-0.59080.5890.2930.5840.0739-0.16411.60290.60760.8068-6.786-107.112388.3991
111.73230.07951.56740.7203-0.59629.5527-0.26321.7527-0.1825-0.43810.25630.64982.15291.61690.31742.6503-0.49620.4692.1044-0.00411.08411.1977-95.058391.2337
12-0.2985-0.1299-0.03581.49131.32070.8095-0.1082-1.033-0.24471.30870.3673-0.63860.38160.5570.07221.25090.03980.56352.1880.08690.4101-18.8135-99.8316122.9042
13-0.1277-0.5552-0.18730.682-0.16210.4334-0.1432-0.49440.15380.71030.16030.4589-0.0586-0.42730.03991.1424-0.1692-0.13512.0022-0.28880.5668-14.7845-7.0996116.3549
140.59880.48571.02140.85211.35012.331-0.36060.1753-0.9339-0.5176-1.06050.3412-4.8843-0.90661.34563.5419-0.2002-0.55822.5517-0.38252.1106-43.1413-16.975984.2671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)A19 - 80
2X-RAY DIFFRACTION1chain A and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)A154 - 274
3X-RAY DIFFRACTION1chain A and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)A344 - 382
4X-RAY DIFFRACTION1chain A and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)A592 - 765
5X-RAY DIFFRACTION1chain A and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)A2001 - 2002
6X-RAY DIFFRACTION2chain A and (resid 383:591)A383 - 591
7X-RAY DIFFRACTION3chain A and (resid 81:153 )A81 - 153
8X-RAY DIFFRACTION4chain A and (resid 275:343 or resid 2003:2005)A275 - 343
9X-RAY DIFFRACTION4chain A and (resid 275:343 or resid 2003:2005)A2003 - 2005
10X-RAY DIFFRACTION5chain A and (resid 766:1016 or segid E)A0
11X-RAY DIFFRACTION6chain C and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)C19 - 80
12X-RAY DIFFRACTION6chain C and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)C154 - 274
13X-RAY DIFFRACTION6chain C and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)C344 - 382
14X-RAY DIFFRACTION6chain C and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)C592 - 765
15X-RAY DIFFRACTION6chain C and (resid 19:80 or resid 154:274 or resid 344:382 or resid 592:765 or resid 2001:2002)C2001 - 2002
16X-RAY DIFFRACTION7chain C and (resid 383:591)C383 - 591
17X-RAY DIFFRACTION8chain C and (resid 81:153 )C81 - 153
18X-RAY DIFFRACTION9chain C and (resid 275:343 or resid 2003:2005)C275 - 343
19X-RAY DIFFRACTION9chain C and (resid 275:343 or resid 2003:2005)C2003 - 2005
20X-RAY DIFFRACTION10chain C and (resid 766:1016 or segid F)C0
21X-RAY DIFFRACTION11chain HH23 - 49
22X-RAY DIFFRACTION12chain DD18 - 303
23X-RAY DIFFRACTION13chain BB18 - 303
24X-RAY DIFFRACTION14chain GG23 - 49

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