[English] 日本語
Yorodumi
- PDB-7x20: Crystal structure of non gastric H,K-ATPase alpha2 in (K+)E2-AlF state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x20
TitleCrystal structure of non gastric H,K-ATPase alpha2 in (K+)E2-AlF state
Components
  • Potassium-transporting ATPase alpha chain 2
  • Sodium/potassium-transporting ATPase subunit beta-1
KeywordsMEMBRANE PROTEIN / P-type ATPase / transporter / proton pump / colon / kidney / airway
Function / homology
Function and homology information


Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / P-type potassium:proton transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / metal ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex ...Basigin interactions / H+/K+-exchanging ATPase / Ion transport by P-type ATPases / P-type potassium:proton transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / metal ion transport / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / regulation of calcium ion transmembrane transport / membrane repolarization / regulation of pH / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / potassium ion homeostasis / intracellular sodium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / relaxation of cardiac muscle / Ion homeostasis / sodium ion transport / organelle membrane / potassium ion import across plasma membrane / monoatomic cation transmembrane transport / ATPase activator activity / blastocyst development / intercalated disc / lateral plasma membrane / sperm flagellum / ATP metabolic process / cardiac muscle contraction / T-tubule / sodium ion transmembrane transport / proton transmembrane transport / protein localization to plasma membrane / potassium ion transport / sarcolemma / caveola / : / intracellular calcium ion homeostasis / ATPase binding / protein-macromolecule adaptor activity / regulation of gene expression / basolateral plasma membrane / response to hypoxia / cell adhesion / protein stabilization / apical plasma membrane / protein heterodimerization activity / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 / Cation-transporting P-type ATPase, C-terminal ...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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / : / Sodium/potassium-transporting ATPase subunit beta-1 / Potassium-transporting ATPase alpha chain 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNakanishi, H. / Abe, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02426 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Structure and function of H/K pump mutants reveal Na/K pump mechanisms.
Authors: Victoria C Young / Hanayo Nakanishi / Dylan J Meyer / Tomohiro Nishizawa / Atsunori Oshima / Pablo Artigas / Kazuhiro Abe /
Abstract: Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na to H selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via ...Ion-transport mechanisms evolve by changing ion-selectivity, such as switching from Na to H selectivity in secondary-active transporters or P-type-ATPases. Here we study primary-active transport via P-type ATPases using functional and structural analyses to demonstrate that four simultaneous residue substitutions transform the non-gastric H/K pump, a strict H-dependent electroneutral P-type ATPase, into a bona fide Na-dependent electrogenic Na/K pump. Conversion of a H-dependent primary-active transporter into a Na-dependent one provides a prototype for similar studies of ion-transport proteins. Moreover, we solve the structures of the wild-type non-gastric H/K pump, a suitable drug target to treat cystic fibrosis, and of its Na/K pump-mimicking mutant in two major conformations, providing insight on how Na binding drives a concerted mechanism leading to Na/K pump phosphorylation.
History
DepositionFeb 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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: Potassium-transporting ATPase alpha chain 2
B: Sodium/potassium-transporting ATPase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0046
Polymers146,6022
Non-polymers4024
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-15 kcal/mol
Surface area56050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.970, 109.060, 267.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Potassium-transporting ATPase alpha chain 2 / HK alpha 2 / Non-gastric H(+)/K(+) ATPase subunit alpha / Non-gastric Na(+)/K(+) ATPase subunit ...HK alpha 2 / Non-gastric H(+)/K(+) ATPase subunit alpha / Non-gastric Na(+)/K(+) ATPase subunit alpha / Proton pump / Sodium pump


Mass: 109084.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Atp12a, Atp1al1 / Production host: Homo sapiens (human)
References: UniProt: P54708, H+/K+-exchanging ATPase, Na+/K+-exchanging ATPase
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 37516.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Atp1b1 / Production host: Homo sapiens (human) / References: UniProt: P07340

-
Sugars , 1 types, 1 molecules

#5: 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 , 3 types, 4 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 33% PEG 300, 50mM Glycine-NaOH pH 9.5, 100mM NaCl, 200mM KCl, 0.1mM AlCl3, 0.4mM NaF

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→48.06 Å / Num. obs: 68181 / % possible obs: 72.54 % / Redundancy: 2 % / Biso Wilson estimate: 49.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 8.36
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.83 / Num. unique obs: 6682 / CC1/2: 0.768

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Coot0.9.1model building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6jxh

6jxh


Resolution: 3.3→48.06 Å / SU ML: 0.5458 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 33.2991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.316 1264 5.07 %
Rwork0.2645 23655 -
obs0.2671 24919 72.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.9 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10019 0 21 1 10041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011510241
X-RAY DIFFRACTIONf_angle_d1.392313880
X-RAY DIFFRACTIONf_chiral_restr0.07471589
X-RAY DIFFRACTIONf_plane_restr0.01081766
X-RAY DIFFRACTIONf_dihedral_angle_d13.653792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.430.5143250.4584540X-RAY DIFFRACTION15.07
3.43-3.590.4713580.3856895X-RAY DIFFRACTION25.43
3.59-3.780.3927820.32811526X-RAY DIFFRACTION42.87
3.78-4.010.34091380.28382586X-RAY DIFFRACTION72.24
4.01-4.320.34341780.2583420X-RAY DIFFRACTION95.9
4.32-4.760.29881940.24043606X-RAY DIFFRACTION99.35
4.76-5.450.27891810.24373624X-RAY DIFFRACTION99.53
5.45-6.860.33422050.2963652X-RAY DIFFRACTION99.82
6.86-48.060.2682030.23873806X-RAY DIFFRACTION99.28
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)
10.267812079513-0.1612228030380.7087829451730.990640262593-1.457642809591.98444591128-0.030876856030.09703520859210.03128276222160.09123748400710.0908285074368-0.110520463442-0.324915176844-0.274747572685-0.05663605181940.3394396857170.1053603410270.1063921059780.20401105419-0.07914659065760.293472873949-14.73370558210.1273591538-40.3635732714
21.771088212650.328505252555-0.9557403938681.43555696244-0.3288656767923.77710352920.05018444827550.764014702950.280728627017-1.243926801430.0517000057561-0.07851779298140.542240087259-0.201419092396-0.1647431774761.126884021250.3043911962580.0389575581290.8637551634610.09802926481590.4631572679237.996083651969.49112440375-79.9241076325
30.446185390908-0.406426045508-0.2969228215760.62067380694-0.5862436434850.9146324337280.1243076623460.1002171763550.0189609977843-0.200395995644-0.05535471615350.03448979856030.5740085875660.231195123213-0.1048825031170.2300120041050.0986526424960.0381785598617-0.207140242966-0.0590007370710.301289836785-4.40311183142-8.34729612142-18.3816114474
41.17925309772-0.00823094932197-0.2747696401891.37854094697-0.1675190101880.0818149827472-0.1660594674910.758093789879-0.514094439665-0.637421294167-0.0633868550450.6210745913110.231957130372-0.1082425559680.0857331843052-0.0632170284001-0.7618358216890.06787284289150.600863396059-0.1369020451740.341666624143-8.50951277979-28.852044371-4.67786371236
50.85920867310.140104567856-0.4006755570280.4239691145330.2654502978361.605316112930.3760408793160.337664538341-0.1388176894670.178635055148-0.3523228831540.1977533045110.0190057014631-0.6270726570450.03553896020.3834728996390.0294921788042-0.2266741522580.701911927760.01499703051240.194547111114-11.0940822236-5.3723422789442.3418443859
64.64939216888-1.06751462349-0.9864173989033.07930611024-0.4375078639553.464081204420.0821171987463-0.5610099321190.2593845459250.456328833120.0495903674203-0.615846278294-0.122992320967-0.000453639805353-0.1399201234960.3507659108710.0996430647816-0.1390708909130.5824861075890.04109482446560.161653573058-1.67768014135-2.2687448446648.1357205845
72.40919127707-0.6493912893740.4138166137562.1619693344-0.4533170224831.63593914763-0.1713667256010.057449039750.131157863802-0.02488824136480.127085691426-0.0538058459483-0.8504833872680.02251708544750.01530222224770.57167715238-0.0301026018388-0.04584352141820.4155927010630.006947850666340.155085094225-7.394876965926.6900900542342.9295532844
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 51 through 462 )AA51 - 4621 - 412
22chain 'A' and (resid 463 through 610 )AA463 - 610413 - 560
33chain 'A' and (resid 611 through 1036 )AA611 - 1036561 - 986
44chain 'B' and (resid 17 through 60 )BC17 - 601 - 44
55chain 'B' and (resid 61 through 131 )BC61 - 13145 - 115
66chain 'B' and (resid 132 through 210 )BC132 - 210116 - 194
77chain 'B' and (resid 211 through 304 )BC211 - 304195 - 288

+
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