[English] 日本語
Yorodumi
- PDB-7d91: Crystal Structure of the Na+,K+-ATPase in the E2P state with boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d91
TitleCrystal Structure of the Na+,K+-ATPase in the E2P state with bound Mg2+ (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
Function / homology
Function and homology information


Basigin interactions / 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 / sodium ion binding / sodium:potassium-exchanging ATPase complex ...Basigin interactions / 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 / sodium ion binding / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / ion channel regulator activity / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / regulation of sodium ion transport / proton transmembrane transport / sarcolemma / transmembrane transport / melanosome / ATPase binding / protein-macromolecule adaptor activity / basolateral plasma membrane / cell adhesion / apical plasma membrane / axon / innate immune response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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/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 / 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 superfamily
Similarity search - Domain/homology
CHOLESTEROL / 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: 3.35 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)164,83821
Polymers154,6873
Non-polymers10,15018
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-27 kcal/mol
Surface area59460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.325, 84.325, 646.360
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

-
Components

-
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

-
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

-
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
#8: 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

-
Non-polymers , 4 types, 20 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.: 2 / 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.: 11 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.88 %
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

-
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: Jan 20, 2019
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 21591 / % possible obs: 58.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 81.78 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.095 / Rrim(I) all: 0.157 / Net I/σ(I): 9.33
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 144 / CC1/2: 0.595 / Rpim(I) all: 0.361 / Rrim(I) all: 0.529 / % possible all: 4.8

-
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: 6KPU

6kpu
PDB Unreleased entry


Resolution: 3.35→14.95 Å / SU ML: 0.4589 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 23.7568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2599 945 5.08 %
Rwork0.2146 17673 -
obs0.2169 18618 53.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.86 Å2
Refinement stepCycle: LAST / Resolution: 3.35→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10372 0 343 4 10719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006210926
X-RAY DIFFRACTIONf_angle_d1.014614828
X-RAY DIFFRACTIONf_chiral_restr0.45011683
X-RAY DIFFRACTIONf_plane_restr0.00693193
X-RAY DIFFRACTIONf_dihedral_angle_d18.42684138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.520.4269140.3198294X-RAY DIFFRACTION6.34
3.53-3.740.455390.3095640X-RAY DIFFRACTION14.08
3.74-4.030.3203600.26791248X-RAY DIFFRACTION26.7
4.03-4.420.25811200.2322252X-RAY DIFFRACTION48.24
4.42-5.040.26622090.21323824X-RAY DIFFRACTION81.72
5.04-6.270.27992390.23734444X-RAY DIFFRACTION92.84
6.27-14.950.22352640.18424971X-RAY DIFFRACTION98.81
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)
10.04443571708190.0179361851666-0.2478193061820.171813459979-0.0233278157876-0.04449017375560.369901632504-0.3492899186450.3098418908790.292835315742-0.6287989636170.3400220291580.0714872900207-0.665256231037.44115457905E-120.4037902319310.635748593613-0.113446072594-0.02646692951640.6476306051530.18192529081425.864071505580.769855395235.7280812447
20.0603858478751-0.0197237849731-0.04402520753810.0701981674095-0.02728909630620.0504531455007-0.00104410947378-0.13636570767-0.09089720577040.0408912716268-0.007729863824580.1197499816040.30584814975-0.210613219368.87848486606E-100.598042646754-0.176503809599-0.1234250102190.8657691859230.2796285141020.69531880466835.784259356955.405983284873.5346055403
3-0.110014452874-0.278590101057-0.0779491979851-0.08484506667790.07876688476450.03553773476450.858426771087-0.8052250697630.4378056569980.449993237541-0.4312871909030.272760573826-0.3828117829680.549859255795-1.12371554471E-100.03954087994870.960938934539-0.377356994124-0.5528062532870.7166615085240.15314753202648.517119663478.971610304917.9548662764
40.001707628082060.003104744803490.001503678293750.001936608502640.00173214118641-0.00106340008656-0.0247367338632-0.02004701966940.0008003054023580.0260129469598-0.02621042757580.004232709419570.00304959777190.01567527657578.45211144552E-81.275205704560.0211678496614-0.0868604900280.965198463574-0.07963579867621.1031484000556.5164317475105.41986946916.7037820288
50.008853373154230.008304935059090.0189547682171-0.003129834011080.00534713301551-0.0116169286090.1700036584280.0811974754476-0.06648463037520.0155823073344-0.134720136459-0.104137008555-0.1184503261730.09946074054522.63845138523E-80.6736999306990.115342618994-0.04608762694630.386011007220.1348441265450.55149605516362.384226596681.4707930709-11.2877125079
60.00803403818303-0.01195553411550.02439208150850.0139779276796-0.003749817663520.00773974670574-0.01795658704510.0860087759560.0262244441929-0.2218691468340.176666470782-0.0656124900082-0.0781994517546-0.0611062919713-8.31623135099E-90.7545075518070.352269323125-0.07791166483660.8821870929170.09836153444080.90154675469548.735020560984.259410098-46.3415764085
70.0236548694553-0.0193921775618-0.00411212977035-0.00782460542095-0.0111268914093-0.003412680131050.06035819221640.177776889088-0.00370976191415-0.03822462161770.01798862837130.1235212925070.0557204673186-0.083852103254-2.36757677757E-80.8132856604170.17238406492-0.1139547802440.9088655042580.09923616140540.76783105645839.847811924374.8755622577-48.1883426863
80.0149931804992-0.000856024134841-0.01358065158280.002764935254360.009265435885570.02762726080680.04793344362870.05037959305460.00398269589498-0.05586679675550.04427193560130.2138888608130.0178352968444-0.166672432024-1.0399534891E-80.6729362694250.226977699278-0.1871260493480.936201091340.09697202853540.69290200181736.330795988777.7207747493-43.0242404712
9-0.000309105912219-0.0008555039143075.17177529461E-50.0002976091994970.0001704188777027.04058797559E-50.000473458360576-0.0078990187866-0.01689361436210.008078986705710.0234782170370.009049512888030.0124961865355-0.004438740832239.68900503371E-60.6020218459740.125744271014-0.04685013584180.633980701169-0.05548029043910.72919736228850.385910371461.3992684317-27.9246202798
100.0009137330428790.000734509162833-0.003577854420790.007992718848680.003632984886810.00118027913691-0.007869435564560.0198116681759-0.0713839071686-0.007534689372990.005444067143140.0999441502954-0.0141747065882-0.0201086055908-7.38567620482E-100.5497130278980.08487745439530.1219451824840.2655126682410.1680561872930.56048884936846.449008178755.5555506809-2.49669198894
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more