[English] 日本語
Yorodumi
- PDB-4hqj: Crystal structure of Na+,K+-ATPase in the Na+-bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hqj
TitleCrystal structure of Na+,K+-ATPase in the Na+-bound state
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • Na+/K+ ATPase gamma subunit transcript variant a
KeywordsHYDROLASE/TRANSPORT PROTEIN / Membrane protein / Na+/K+ transport / HYDROLASE-TRANSPORT PROTEIN complex
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 / membrane repolarization / sodium ion binding ...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 / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / establishment or maintenance of transmembrane electrochemical gradient / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / ATPase activator activity / potassium ion binding / sodium channel regulator activity / regulation of sodium ion transport / proton transmembrane transport / sarcolemma / transmembrane transport / melanosome / protein-macromolecule adaptor activity / ATPase binding / 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. / Sodium and potassium ATPases beta subunits signature 2. ...: / : / 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
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / CHOLESTEROL / 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 / SIRAS / Resolution: 4.3 Å
AuthorsNyblom, M. / Reinhard, L. / Gourdon, P. / Nissen, P.
CitationJournal: Science / Year: 2013
Title: Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state.
Authors: Nyblom, M. / Poulsen, H. / Gourdon, P. / Reinhard, L. / Andersson, M. / Lindahl, E. / Fedosova, N. / Nissen, P.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references

-
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: Na+/K+ ATPase gamma subunit transcript variant a
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,25223
Polymers310,0726
Non-polymers3,18017
Water0
1
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,43311
Polymers155,0363
Non-polymers1,3978
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-78 kcal/mol
Surface area57610 Å2
MethodPISA
2
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,81912
Polymers155,0363
Non-polymers1,7839
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-80 kcal/mol
Surface area58240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.073, 219.578, 261.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 32:258 OR RESSEQ 273:397 OR RESSEQ 403:822 OR RESSEQ 827:1016 )
211CHAIN C AND (RESSEQ 32:258 OR RESSEQ 273:397 OR RESSEQ 403:822 OR RESSEQ 827:1016 )
112CHAIN B AND (RESSEQ 22:167 OR RESSEQ 169:193 OR RESSEQ 197:303 )
212CHAIN D AND (RESSEQ 22:167 OR RESSEQ 169:193 OR RESSEQ 197:303 )
113CHAIN G AND (RESSEQ 23:47 )
213CHAIN E AND (RESSEQ 23:47 )

NCS ensembles :
ID
1
2
3

-
Components

-
Sodium/potassium-transporting ATPase subunit ... , 2 types, 4 molecules ACBD

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


Mass: 112797.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05024, EC: 3.6.3.9
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35144.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05027

-
Protein , 1 types, 2 molecules GE

#3: Protein Na+/K+ ATPase gamma subunit transcript variant a


Mass: 7094.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q58K79

-
Non-polymers , 5 types, 17 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O

-
Details

Sequence detailsTHE EXPERIMENTAL INFO OF UNIPROT (P05027, AT1B1_PIG) SHOWS CONFLICT AT THIS POSITION: F -> S (IN ...THE EXPERIMENTAL INFO OF UNIPROT (P05027, AT1B1_PIG) SHOWS CONFLICT AT THIS POSITION: F -> S (IN REF. 1; CAA27575).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 5.06 Å3/Da / Density % sol: 75.68 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% PEG2KMME, 150mM NaCl, 6% glycerol, 6% MPD, 25mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA21.1008
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELNov 19, 2010
PSI PILATUS 6M2PIXELAug 14, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Fixed-exit LN2 cooled Double Crystal Monochromator, Crystal type Si(111)SINGLE WAVELENGTHMx-ray1
2Fixed-exit LN2 cooled Double Crystal Monochromator, Crystal type Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.10081
ReflectionResolution: 4.3→55 Å / Num. all: 43619 / Num. obs: 43585 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 4.3 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
remdaq.pilatusdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 4.3→11.999 Å / SU ML: 0.62 / σ(F): 2.01 / Phase error: 31.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 2080 5.02 %RANDOM
Rwork0.2612 ---
all0.2625 ---
obs0.2626 41407 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.3→11.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20359 0 212 0 20571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721048
X-RAY DIFFRACTIONf_angle_d1.12528551
X-RAY DIFFRACTIONf_dihedral_angle_d15.667782
X-RAY DIFFRACTIONf_chiral_restr0.0833236
X-RAY DIFFRACTIONf_plane_restr0.0053640
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A7468X-RAY DIFFRACTIONPOSITIONAL
12C7468X-RAY DIFFRACTIONPOSITIONAL0.031
21B2271X-RAY DIFFRACTIONPOSITIONAL
22D2271X-RAY DIFFRACTIONPOSITIONAL0.028
31G188X-RAY DIFFRACTIONPOSITIONAL
32E188X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
4.3001-4.39530.3741470.36722576
4.3953-4.49950.34741320.34092604
4.4995-4.61450.37311390.33752586
4.6145-4.74210.3391410.33132614
4.7421-4.88520.31721300.32522592
4.8852-5.04720.31461380.32362586
5.0472-5.23310.37391350.32682625
5.2331-5.44990.37341390.32522627
5.4499-5.70770.32991420.31052604
5.7077-6.02240.35821360.30222610
6.0224-6.42050.32731360.27682646
6.4205-6.95030.27841420.25332622
6.9503-7.7140.24711390.21722664
7.714-8.98490.20631420.18322663
8.9849-11.99950.20091420.1682708
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)
11.3946-0.86990.75157.38820.40588.71640.495-0.8160.33660.6679-0.3546-0.0532-0.4799-0.0501-0.23790.9006-0.06440.11531.36360.01191.372641.668956.796922.6695
21.6902-0.93664.31936.17010.03167.39530.195-0.2356-0.13730.0475-0.310.4811-0.4343-0.35050.23150.91860.02380.20661.27310.23751.183310.493742.37215.9748
36.89641.51540.42526.58531.51774.8494-0.6511.4376-0.0117-1.09680.4692-0.4533-0.45820.65420.15181.1008-0.0574-0.01251.47230.01130.975230.739840.5525-5.433
43.20040.3623-2.06872.38861.44675.36060.0422-0.16220.26731.16540.10530.30250.4054-0.1888-0.18561.74820.19450.24151.1660.29971.07833.648643.063262.1198
58.1454-2.9524-4.53497.79826.11365.4867-1.9714-0.1144-0.2117-0.2135-1.88153.2318-0.2136-0.82961.97181.0788-0.77210.15321.3220.25442.371722.639843.67956.73
65.20890.4639-0.36292.6442-1.10296.33950.1835-0.1242-0.27190.32550.09620.13670.02881.1-0.29991.5615-0.1435-0.11811.9234-0.31181.83574.621982.537311.576
75.18072.58362.12396.749-0.2280.8341-0.20270.9386-0.5404-0.09840.5478-1.3387-0.39321.6247-0.37391.7817-0.33410.32.5435-0.66561.821727.8225105.422424.1583
86.7841.3599-2.36961.95530.90162.47070.01251.26530.0997-1.50960.6327-0.9597-1.00390.859-0.78143.0817-0.60010.63043.5248-0.50412.365728.022101.4099-5.1586
92.4133-0.4184-1.3672.3617-0.08019.04130.3173-0.00580.07330.52590.21070.1749-0.22670.2513-0.37851.6534-0.18960.24251.4026-0.37911.37971.0401106.644662.3371
103.55163.3526-0.04354.01322.10115.59140.0313-3.9711.93820.9981-2.8350.0205-1.52480.3433.3522.5668-0.7683-0.40832.6552-0.43532.541225.9662100.81369.7959
116.22820.05893.72823.5383-2.46585.31730.27311.81910.56410.3067-2.2126-0.327-0.29131.37041.85082.04660.57040.57031.90580.05531.8909-18.655641.558458.6032
123.20170.13-0.28041.46641.83593.740.2567-1.0636-0.1181.2226-0.3616-0.04160.47590.06020.04674.105-0.26510.68192.64430.16292.3057-11.041247.444107.7523
130.0887-0.3211-0.2350.9521-0.15136.71150.29550.260.0955-0.237-0.23390.3805-0.1319-0.05240.012.8932-0.2546-0.0218-0.25932.88364.27623.394225.829370.3844
141.9923-0.973-0.520.6852.40079.3429-1.65222.64911.17270.31340.8018-1.65420.4235-1.09470.67064.6915-0.94330.39041.73690.85622.9158-12.111127.52772.1966
155.7241-0.8363-2.38325.61474.67324.227-0.30510.29050.87020.0474-0.30060.82973.0004-0.49060.35512.2388-0.013-0.08131.28880.26841.60112.026326.48574.6818
164.6097-4.2183-2.76337.44251.99379.04380.7857-0.5588-0.82250.0231-1.1560.4138-0.74221.58630.15122.0163-0.4523-0.01042.2491-0.19771.362518.5523114.211474.0821
172.35930.021-0.88893.9618-0.64352.5494-0.0042-0.6307-0.08030.8923-0.28511.11740.3018-0.2460.23593.4353-0.11620.78472.5624-0.19362.4163-19.2097105.8178105.8344
184.06171.4825-4.43890.9819-0.91566.00520.50680.08540.435-0.0987-1.89852.94050.81310.45210.75723.7763-0.4911-1.4742.6607-0.05174.31819.2441105.329667.8827
194.7785-1.9144-5.92411.14012.24747.31321.00840.05110.02840.9055-0.61410.28410.90140.50250.63153.94851.572-0.4271.4279-2.14471.5147-8.8666123.287365.3669
202.98-0.99461.21363.7443-4.12314.48470.03520.45561.84340.0553-1.1838-1.47590.21220.0980.22944.72371.4672-1.37482.4703-0.78674.36711.0979127.086674.706
212.84652.15651.9393.6475-1.83455.3010.49880.0891-0.42630.6014-0.15971.23850.9322-0.9362-0.72132.60750.19940.26031.7139-0.00442.0159-17.7531119.718365.0498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 32:91 OR RESID 158:274)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 348:376 OR RESID 590:747)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 377:589)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 92:157 OR RESID 275:347 OR RESID 748:1016 OR RESID 1104:1106)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1101:1103)
6X-RAY DIFFRACTION6CHAIN C AND (RESID 30:91 OR RESID 158:274)
7X-RAY DIFFRACTION7CHAIN C AND (RESID 348:376 OR RESID 590:747)
8X-RAY DIFFRACTION8CHAIN C AND (RESID 377:589)
9X-RAY DIFFRACTION9CHAIN C AND (RESID 92:157 OR RESID 275:347 OR RESID 748:1016 OR RESID 1104:1106)
10X-RAY DIFFRACTION10CHAIN C AND (RESID 1101:1103)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 22:64)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 65:303)
13X-RAY DIFFRACTION13CHAIN A AND (RESID 1107:1107)
14X-RAY DIFFRACTION14CHAIN A AND (RESID 1108:1108)
15X-RAY DIFFRACTION15CHAIN G
16X-RAY DIFFRACTION16CHAIN D AND (RESID 22:64)
17X-RAY DIFFRACTION17CHAIN D AND (RESID 65:303)
18X-RAY DIFFRACTION18CHAIN D AND (RESID 400:400)
19X-RAY DIFFRACTION19CHAIN C AND (RESID 1107:1107)
20X-RAY DIFFRACTION20CHAIN C AND (RESID 1108:1108)
21X-RAY DIFFRACTION21CHAIN E

+
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