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- PDB-3a3y: Crystal structure of the sodium-potassium pump with bound potassi... -

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Basic information

Entry
Database: PDB / ID: 3a3y
TitleCrystal structure of the sodium-potassium pump with bound potassium and ouabain
Components
  • NA+,K+-ATPASE BETA SUBUNIT
  • Na, K-ATPase alpha subunit
  • Phospholemman-like protein
KeywordsHYDROLASE/TRANSPORT PROTEIN / MEMBRANE PROTEIN / ION PUMP / ATPASE / K+ BINDING / OUABAIN BINDING / HALOACID DEHYDROGENEASE SUPERFAMILY / PHOSPHATE ANALOGUE / ATP-BINDING / HYDROLASE / ION TRANSPORT / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / HYDROLASE-TRANSPORT PROTEIN COMPLEX / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane ...regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / 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 / Sodium/potassium-transporting ATPase subunit beta ...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-) / OUABAIN / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit alpha / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSqualus acanthias (spiny dogfish)
SQUALUS ACANTHIAS (spiny dogfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOgawa, H. / Shinoda, T. / Cornelius, F. / Toyoshima, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of the sodium-potassium pump (Na+,K+-ATPase) with bound potassium and ouabain.
Authors: Ogawa, H. / Shinoda, T. / Cornelius, F. / Toyoshima, C.
History
DepositionJun 23, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate 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: Na, K-ATPase alpha subunit
B: NA+,K+-ATPASE BETA SUBUNIT
G: Phospholemman-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,58713
Polymers156,7103
Non-polymers1,87710
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-37 kcal/mol
Surface area56180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.884, 50.720, 163.342
Angle α, β, γ (deg.)90.00, 104.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABG

#1: Protein Na, K-ATPase alpha subunit


Mass: 113309.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q4H132
#2: Protein NA+,K+-ATPASE BETA SUBUNIT


Mass: 35175.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SQUALUS ACANTHIAS (spiny dogfish) / References: UniProt: C4IX13*PLUS
#3: Protein Phospholemman-like protein


Mass: 8225.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q70Q12

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Sugars , 1 types, 3 molecules

#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 73 molecules

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


Mass: 100.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F4Mg
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-OBN / OUABAIN / Ouabain


Mass: 584.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H44O12
#8: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THE CHAIN B DOES NOT CURRENTLY EXIST IN UNIPROT.

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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: 2.85 Å3/Da / Density % sol: 56.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 44358 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 30.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4350 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.878 / SU B: 40.906 / SU ML: 0.361 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.859 / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2928 1333 3 %RANDOM
Rwork0.24715 ---
obs0.24855 42690 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.075 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å20 Å2-1.02 Å2
2---1.29 Å20 Å2
3----3.65 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10122 0 120 66 10308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.98214190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67251290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07124.089450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.845151783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.471563
X-RAY DIFFRACTIONr_chiral_restr0.0790.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217787
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9281.56435
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.519210404
X-RAY DIFFRACTIONr_scbond_it1.36834021
X-RAY DIFFRACTIONr_scangle_it2.0724.53786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 81 -
Rwork0.338 3052 -
obs--99.9 %
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)
11.1590.8304-0.03031.86670.42571.09910.0293-0.0161-0.01580.16190.0245-0.08740.15640.1763-0.05380.03450.0287-0.04080.16550.0290.1838150.520640.160465.9105
20.9625-0.3765-0.26152.52430.583.6905-0.2075-0.0482-0.09130.3378-0.06170.4081-0.0674-0.30960.26920.08480.01610.0760.0855-0.02020.2309112.189639.003177.473
30.32260.1193-0.03920.9841-0.43751.2709-0.01030.02860.0299-0.0431-0.00070.04550.14350.0650.0110.0420.0188-0.02930.1280.00240.1878132.16218.977954.8715
40.0635-0.081-0.02940.27720.20121.24160.00770.02240.03940.0202-0.0301-0.05370.08340.11870.02240.09470.0182-0.00490.18280.02550.1355129.719314.69796.2859
50.3982-0.0639-0.97752.24133.56347.6844-0.0263-0.0560.3384-0.0230.25720.3431-0.10570.7801-0.23090.2624-0.1455-0.0570.61580.05720.3716149.105828.506714.75
61.9558-0.2429-0.24661.0399-0.25392.8020.18150.50680.2291-0.4325-0.2479-0.1363-0.06010.31960.06640.34740.09780.11770.45830.12390.0663142.427920.6871-37.3312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 81
2X-RAY DIFFRACTION1A157 - 276
3X-RAY DIFFRACTION2A384 - 594
4X-RAY DIFFRACTION3A355 - 383
5X-RAY DIFFRACTION3A595 - 754
6X-RAY DIFFRACTION4A277 - 354
7X-RAY DIFFRACTION4A755 - 1023
8X-RAY DIFFRACTION4B35 - 72
9X-RAY DIFFRACTION4G8 - 46
10X-RAY DIFFRACTION5A82 - 156
11X-RAY DIFFRACTION6B73 - 305

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