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- PDB-7d92: Crystal Structure of the Na+,K+-ATPase in the E2P state with boun... -

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Basic information

Entry
Database: PDB / ID: 7d92
TitleCrystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ and anthroylouabain (P4(3)2(1)2 symmetry)
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • FXYD domain-containing ion transport regulator
KeywordsTRANSPORT PROTEIN / Na+ / K+-ATPase / membrane protein / ion transport / Cardiotonic steroids
Function / homology
Function and homology information


Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / Ion transport by P-type ATPases / positive regulation of sodium ion export across plasma membrane / regulation of monoatomic ion transport / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex ...Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / Ion transport by P-type ATPases / positive regulation of sodium ion export across plasma membrane / regulation of monoatomic ion transport / positive regulation of potassium ion import across plasma membrane / sodium ion binding / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / positive regulation of potassium ion transmembrane transport / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / ion channel regulator activity / relaxation of cardiac muscle / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of sodium ion transmembrane transport / organelle membrane / potassium ion import across plasma membrane / potassium ion binding / intracellular potassium ion homeostasis / ATPase activator activity / intercalated disc / lateral plasma membrane / sperm flagellum / transporter activator activity / 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 / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / cell adhesion / protein stabilization / apical plasma membrane / axon / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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. ...: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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 / 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 / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
CHOLESTEROL / Chem-H0C / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 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 / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsKanai, R. / Cornelius, F. / Ogawa, H. / Motoyama, K. / Vilsen, B. / Toyoshima, C.
Funding support Japan, Denmark, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K18500 Japan
Japan Society for the Promotion of Science (JSPS)16H02499 Japan
Japan Society for the Promotion of Science (JSPS)19H00975 Japan
Danish Council for Independent ResearchDFF7016-00193B Denmark
Danish Council for Independent ResearchDFF4183-00011A Denmark
Novo Nordisk FoundationNNF13OC0013409 Denmark
Novo Nordisk FoundationNNF13OC0006555 Denmark
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Binding of cardiotonic steroids to Na + ,K + -ATPase in the E2P state.
Authors: Kanai, R. / Cornelius, F. / Ogawa, H. / Motoyama, K. / Vilsen, B. / Toyoshima, C.
History
DepositionOct 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: FXYD domain-containing ion transport regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,65220
Polymers154,6873
Non-polymers8,96417
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-83 kcal/mol
Surface area60110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.234, 84.234, 646.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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

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


Mass: 112388.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05024, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35204.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05027

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Protein , 1 types, 1 molecules G

#3: Protein FXYD domain-containing ion transport regulator / Na+/K+ ATPase gamma subunit transcript variant a


Mass: 7094.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q58K79

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Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-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
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-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: obtained synthetically / 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, 22 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#8: Chemical ChemComp-H0C / [(2~{R},3~{R},4~{R},5~{S},6~{S})-2-[[(1~{R},3~{S},5~{S},8~{R},9~{S},10~{R},11~{R},13~{R},14~{S},17~{R})-10-(hydroxymethyl)-13-methyl-1,5,11,14-tetrakis(oxidanyl)-17-(5-oxidanylidene-2~{H}-furan-3-yl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]-6-methyl-3,5-bis(oxidanyl)oxan-4-yl] anthracene-9-carboxylate


Mass: 788.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H52O13 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 175 mM MgCl2, 18% (w/v) PEG2000MME, 10% (w/v) glycerol, 5 mM GSH, 0.1 mM DTT and 1 mg/ml butylhydroxytoluen, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2020
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 9668 / % possible obs: 41.5 % / Redundancy: 10.8 % / Biso Wilson estimate: 112.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.07 / Rrim(I) all: 0.231 / Net I/σ(I): 11.85
Reflection shellResolution: 3.9→4.01 Å / Redundancy: 8.9 % / Rmerge(I) obs: 2.077 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 105 / CC1/2: 0.269 / Rpim(I) all: 0.727 / Rrim(I) all: 2.205 / % possible all: 6.2

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Processing

Software
NameVersionClassification
BSSdata collection
DENZOdata reduction
SCALEPACKdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D91

7d91


Resolution: 3.9→14.94 Å / SU ML: 0.5005 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.0145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2566 459 5 %
Rwork0.209 8716 -
obs0.2113 9175 41.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 149.46 Å2
Refinement stepCycle: LAST / Resolution: 3.9→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10372 0 362 7 10741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004610959
X-RAY DIFFRACTIONf_angle_d0.876814893
X-RAY DIFFRACTIONf_chiral_restr0.3821698
X-RAY DIFFRACTIONf_plane_restr0.0063191
X-RAY DIFFRACTIONf_dihedral_angle_d17.99024160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.450.3535390.324745X-RAY DIFFRACTION10.85
4.45-5.560.3344920.27151752X-RAY DIFFRACTION25.32
5.56-14.940.23733280.19126219X-RAY DIFFRACTION85.62
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)
10.2057313479120.244180135051-0.433344402293-0.04126435557020.09975897985730.2991114965990.215599404615-0.0329256070170.0774477231930.0888523141933-0.1272704854050.0662390022303-0.250562535226-0.2016635124042.35930169232E-101.328031022320.1731019894240.00664481327221.225415225040.1424275683331.1714576014425.382646651179.997530372835.4717297248
20.6360114206650.06571345840390.03281376441410.510757481358-0.1918791209550.01868932439290.0580789231697-0.2458826029370.107646873278-0.0465626414251-0.1848835244110.1294528570140.573053893466-0.121132982106-4.27426263416E-101.4949600208-0.1682619788040.01209882692881.484020447580.1998109930691.4599353129735.103450980755.326859725173.556361762
30.002506048499250.0467702103674-0.214787992339-0.1653535217530.1378382659490.2819842094030.0681781701207-0.0855963785699-0.003626789919190.04011670790910.05181519368130.078977930715-0.1263149206850.141192593137-1.20797451225E-101.308439592320.0885823627741-0.06986956778551.216220571790.1089544418681.2021375062248.050429677678.173977367317.8441796149
4-0.00268957374657-0.04597724090290.00659757465275-0.0106774897428-0.016441424033-0.00177630955933-0.06529398114170.01593627690430.160992550970.3633741160780.407556738421-0.6556569662860.14147797028-0.223539433998-1.86189456593E-61.70831783174-0.1818661484480.1264693459521.67267139592-0.0642798108531.2353616013855.5183451209104.30875577317.4735550883
50.321287450989-0.1197486606840.0904664965748-0.1658907457310.279530921077-0.168817751589-0.06553577320310.1166742762820.372077615349-0.1434819043490.07159955239320.286632164231-0.3483479939840.008485080339641.1055562324E-71.35730115519-0.203259421145-0.02600745433610.9217654796280.01436720485771.2441799831361.844673546580.7790735111-11.0976176173
60.0509919196887-0.251621923902-0.195147283617-0.0083831898051-0.2114449317270.0468331237497-0.06141856762120.830252922627-0.0884786937391-0.435140317507-0.0153542292551-0.132794797991-0.28467994223-0.6443786134041.56214031784E-81.266000672420.100384762143-0.09640898340481.89749753260.1191611359361.5646408763648.566910642684.2565743375-46.2103610093
70.1278929372910.228840762776-0.168374629478-0.0484708359871-0.152216199780.0009313094097050.2419931640810.420498896456-0.057530802976-0.346775834451-0.171140137578-0.0976120542073-0.0985791903068-0.3194814660167.02367026452E-91.120083512370.0711573878045-0.07738880744651.68804519797-0.1767135809861.5072447101739.654985709674.9679755518-48.2454905128
8-0.107106392010.09651278924610.2349130473150.1556477791530.1625647052580.02520337510890.398876171037-0.144186518926-0.374028372308-0.497388499885-0.2090287103480.147274214866-0.489580401905-0.0190184573718-1.5176957217E-91.429180684760.0780853615457-0.1693118430031.80125710652-0.07160955623911.4708260593536.111589572177.7761704092-43.0872911879
90.001195087295310.003578775291480.003715400629960.00940412071740.0004752802569720.01421391238410.0109154668345-0.1601565837280.03133844272470.181333361713-0.09969230175420.2502479207220.050390368099-0.186228139111-1.78494091035E-51.69064758928-0.1800080275890.08121740598651.264235485120.4261283522251.6006041731350.512996330161.2160884035-28.1054003081
10-0.04010259516660.043337594217-0.02390867231530.08142870012940.02962065401880.00323564881744-0.5557634857670.01786352330070.17057163213-0.6228423153070.2154194991050.8552216658660.03005236853040.00932439643478-3.84769262311E-71.150097514430.0238851816466-0.1176069896371.283346917160.1110162917691.4360687277345.886828632554.9239453476-2.90955001979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 392 )
2X-RAY DIFFRACTION2chain 'A' and (resid 393 through 591 )
3X-RAY DIFFRACTION3chain 'A' and (resid 592 through 1016 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 28 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 160 )
7X-RAY DIFFRACTION7chain 'B' and (resid 161 through 214 )
8X-RAY DIFFRACTION8chain 'B' and (resid 215 through 303 )
9X-RAY DIFFRACTION9chain 'G' and (resid 17 through 22 )
10X-RAY DIFFRACTION10chain 'G' and (resid 23 through 48 )

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