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- PDB-2zxe: Crystal structure of the sodium - potassium pump in the E2.2K+.Pi... -

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Basic information

Entry
Database: PDB / ID: 2zxe
TitleCrystal structure of the sodium - potassium pump in the E2.2K+.Pi state
Components
  • Na+,K+-ATPase beta subunit
  • Na, K-ATPase alpha subunit
  • Phospholemman-like protein
KeywordsHYDROLASE/TRANSPORT PROTEIN / membrane protein / ion pump / ATPase / K+ binding / Haloacid dehydrogenease superfamily / phosphate analogue / ATP-binding / Hydrolase / Ion transport / Nucleotide-binding / Phosphoprotein / HYDROLASE-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / ATPase activator activity / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / sodium channel regulator activity / proton transmembrane transport ...regulation of monoatomic ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / ATPase activator activity / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / sodium channel regulator activity / proton transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Na, k-atpase alpha subunit. / 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 ...Na, k-atpase alpha subunit. / 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 / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CHOLESTEROL / : / TETRAFLUOROMAGNESATE(2-) / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsShinoda, T. / Ogawa, H. / Cornelius, F. / Toyoshima, C.
CitationJournal: Nature / Year: 2009
Title: Crystal structure of the sodium - potassium pump at 2.4 A resolution
Authors: Shinoda, T. / Ogawa, H. / Cornelius, F. / Toyoshima, C.
History
DepositionDec 22, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.3Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_modification_feature / pdbx_nonpoly_atom_coordination ...pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
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: Na, K-ATPase alpha subunit
B: Na+,K+-ATPase beta subunit
G: Phospholemman-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,98611
Polymers156,7113
Non-polymers1,2748
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-37 kcal/mol
Surface area55460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.815, 50.914, 163.786
Angle α, β, γ (deg.)90.00, 105.12, 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 / 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) / Secretion: rectal gland / References: UniProt: Q4H132
#2: Protein Na+,K+-ATPase beta subunit


Mass: 35176.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / Secretion: rectal gland / References: UniProt: C4IX13*PLUS
#3: Protein Phospholemman-like protein / FXYD10


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

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Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 5 types, 136 molecules

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


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


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


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-CLR / CHOLESTEROL


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


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 4

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 298 K / Method: dialysis / pH: 7 / Details: pH 7.0, Dialysis, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
RAYONIX MX225HE2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 70710 / Num. obs: 70074 / % possible obs: 99.1 % / Redundancy: 17 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 38.8
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5155 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: 3B8E

3b8e


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.924 / SU B: 21.123 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27124 3555 5.1 %RANDOM
Rwork0.24644 ---
obs0.24772 66157 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.782 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å2-1.99 Å2
2--0.01 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10131 0 79 130 10340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210422
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.97714133
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.08451291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77524.102451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.955151785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7871563
X-RAY DIFFRACTIONr_chiral_restr0.0680.21607
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217797
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_it0.5641.56440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.032210412
X-RAY DIFFRACTIONr_scbond_it0.86333982
X-RAY DIFFRACTIONr_scangle_it1.4674.53721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 268 -
Rwork0.349 4590 -
obs--100 %
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)
12.02721.57490.51692.78860.71971.27750.06040.0006-0.06590.12190.053-0.16250.07440.1919-0.11350.01020.0089-0.02390.07040.00570.0838150.251540.032565.9876
21.0445-0.3679-0.11372.17970.89895.5221-0.3256-0.0609-0.15610.2963-0.1740.5471-0.1651-0.4530.49960.13610.02360.09630.0499-0.05220.2237111.911838.94677.8546
30.34290.0544-0.01971.0392-0.43371.08110.02520.06060.038-0.04120.0110.05120.10350.0401-0.03620.11080.0071-0.01950.03230.00380.0961131.886318.913755.2482
40.2187-0.0240.15190.11840.17292.04890.050.10030.01520.0282-0.0033-0.03330.11570.2503-0.04670.08670.051-0.01970.1665-0.00380.0128132.675616.79387.9076
53.57260.3568-0.57381.3890.20042.66620.20020.97790.2456-0.3613-0.2867-0.2372-0.2132-0.00970.08650.25340.18790.11570.63760.17990.0888143.364520.8554-36.9445
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 DIFFRACTION3A2001 - 2002
7X-RAY DIFFRACTION4A82 - 156
8X-RAY DIFFRACTION4A277 - 354
9X-RAY DIFFRACTION4A755 - 1023
10X-RAY DIFFRACTION4B35 - 72
11X-RAY DIFFRACTION4G8 - 46
12X-RAY DIFFRACTION4A2003
13X-RAY DIFFRACTION4A3001
14X-RAY DIFFRACTION5B73 - 305
15X-RAY DIFFRACTION5B4001 - 4021

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