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- PDB-4xe5: Crystal structure of the Na,K-ATPase from bovine -

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Basic information

Entry
Database: PDB / ID: 4xe5
TitleCrystal structure of the Na,K-ATPase from bovine
Components(Sodium/potassium-transporting ATPase subunit ...) x 3
KeywordsHYDROLASE / alpha-helical transmembrane protein / ATPase / sodium ion transport / potassium ion transport / ATP binding / sodium binding / receptor for cardiotonic steroids / plasma membrane / membrane protein / multisubunit complex / beryllium trifluoride
Function / homology
Function and homology information


Basigin interactions / Ion transport by P-type ATPases / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion homeostasis / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / sodium ion export across plasma membrane ...Basigin interactions / Ion transport by P-type ATPases / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion homeostasis / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / sodium ion export across plasma membrane / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / intracellular potassium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / relaxation of cardiac muscle / sodium ion transport / organelle membrane / potassium ion import across plasma membrane / ATPase activator activity / sperm flagellum / intercalated disc / sodium channel regulator activity / lateral plasma membrane / ATP metabolic process / regulation of sodium ion transport / cardiac muscle contraction / T-tubule / proton transmembrane transport / protein localization to plasma membrane / potassium ion transport / sarcolemma / intracellular calcium ion homeostasis / melanosome / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / protein stabilization / apical plasma membrane / membrane raft / axon / protein kinase binding / ATP hydrolysis activity / ATP binding / metal ion 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. / P-type ATPase subfamily IIC, subunit alpha / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / HAD superfamily/HAD-like / 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 / 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 / OUABAIN / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit gamma / Sodium/potassium-transporting ATPase subunit alpha-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.901 Å
AuthorsGregersen, J.L. / Mattle, D. / Fedosova, N.U. / Nissen, P. / Reinhard, L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Isolation, crystallization and crystal structure determination of bovine kidney Na(+),K(+)-ATPase.
Authors: Gregersen, J.L. / Mattle, D. / Fedosova, N.U. / Nissen, P. / Reinhard, L.
History
DepositionDec 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Database references
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
G: Sodium/potassium-transporting ATPase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8769
Polymers154,4453
Non-polymers1,4316
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-70 kcal/mol
Surface area57700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.750, 301.070, 242.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Sodium/potassium-transporting ATPase subunit ... , 3 types, 3 molecules ABG

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


Mass: 112824.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: BFD374 is an aspartate 374 that is covalently modified with beryllium fluoride
Source: (natural) Bos taurus (domestic cattle) / Organ: Kidney / References: UniProt: Q08DA1, EC: 3.6.3.9
#2: Protein Sodium/potassium-transporting ATPase subunit beta


Mass: 35068.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Kidney / References: UniProt: G3MWR4
#3: Protein Sodium/potassium-transporting ATPase subunit gamma / Na(+)/K(+) ATPase subunit gamma / FXYD domain-containing ion transport regulator 2 / Sodium pump gamma chain


Mass: 6552.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Kidney / References: UniProt: Q04645

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Non-polymers , 4 types, 11 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-OBN / OUABAIN


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


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: PEG 3,350, manganese chloride, 3-(N-morpholino)propansulfonic acid (pH adjusted with N-Methyl-D-glucamin), 2-Mercaptoethanol, Octaethylene glycol monododecyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→30 Å / Num. obs: 15157 / % possible obs: 59.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 9.6
Reflection shellHighest resolution: 3.7 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HYT

4hyt


Resolution: 3.901→29.74 Å / SU ML: 0.78 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 36.79 / Stereochemistry target values: ML
Details: data was anisotropically truncated using the Diffraction Anisotropy Server (http://services.mbi.ucla.edu/anisoscale/)
RfactorNum. reflection% reflection
Rfree0.3363 731 5.08 %
Rwork0.3224 --
obs0.3231 14398 64.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.901→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10257 0 100 5 10362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610599
X-RAY DIFFRACTIONf_angle_d0.90614378
X-RAY DIFFRACTIONf_dihedral_angle_d14.0183898
X-RAY DIFFRACTIONf_chiral_restr0.0321636
X-RAY DIFFRACTIONf_plane_restr0.0041833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9005-4.20090.4576630.43411087X-RAY DIFFRACTION26
4.2009-4.62230.38041100.42731842X-RAY DIFFRACTION44
4.6223-5.28790.43611470.3862686X-RAY DIFFRACTION65
5.2879-6.64990.36711750.35943739X-RAY DIFFRACTION88
6.6499-29.74130.25882360.2444313X-RAY DIFFRACTION99
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)
12.4122-1.4919-0.12481.7473-0.8040.9693-0.18911.0143-0.0829-1.4803-0.2565-0.46930.57940.4874-0.11412.42150.25430.29920.7343-0.18931.97251.7808-58.4506-42.2949
21.9851-1.6515-1.26872.16140.89891.29490.5360.2864-0.4249-0.4667-0.80240.6610.3818-0.7851-0.00321.25910.3432-0.05610.95950.17490.9498-18.5449-50.8104-23.4906
32.3486-0.8153-1.65573.429-1.89593.0521-0.1115-0.1103-0.73140.04940.0146-0.37540.3607-0.3692-0.00141.43320.37050.25041.2380.31941.9215.5803-74.635-10.9655
41.154-0.96280.38233.5602-0.07541.11380.17610.0222-0.2207-1.2115-0.04440.17340.128-0.29280.03260.56630.03480.0141.02220.44250.7552-24.2229-5.0015-21.602
50.4159-0.4595-0.7334.15041.59021.12860.5620.32570.7255-0.9857-0.3771-0.2432-1.35670.13570.10751.4370.4936-0.15661.36040.36390.9455-26.099941.5352-30.8703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 27:85 or resseq 160:280)
2X-RAY DIFFRACTION2chain A and (resseq 354:381 or resseq 594:751 )
3X-RAY DIFFRACTION3chain A and resseq 382:593
4X-RAY DIFFRACTION4chain A and (resseq 86:159 or resseq 281:353 or resseq 752:1021 ) or chain B and resseq 19:62 or chain G
5X-RAY DIFFRACTION5chain B and (resseq 63:299 )

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