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- EMDB-37391: Cryo-EM structure of the gastric proton pump Y799W/E936Q mutant i... -

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Basic information

Entry
Database: EMDB / ID: EMD-37391
TitleCryo-EM structure of the gastric proton pump Y799W/E936Q mutant in K+-occluded (K+)E2-AlF state
Map data
Sample
  • Complex: alpha-beta complex of the gastric proton pump
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha
    • Protein or peptide: Potassium-transporting ATPase subunit beta
  • Ligand: POTASSIUM IONPotassium
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsP-type ATPase / gastric proton pump / membrane protein / primary transporter / transporter
Function / homology
Function and homology information


regulation of proton transport / pH reduction / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane ...regulation of proton transport / pH reduction / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / ATPase activator activity / potassium ion transmembrane transport / proton transmembrane transport / cell adhesion / response to xenobiotic stimulus / apical plasma membrane / magnesium ion binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / 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 ...Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / 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
Sodium/potassium-transporting ATPase subunit alpha / Potassium-transporting ATPase subunit beta
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsAbe K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02426 Japan
CitationJournal: J Biol Chem / Year: 2024
Title: Specific protonation of acidic residues confers K selectivity to the gastric proton pump.
Authors: Hridya Valia Madapally / Kazuhiro Abe / Vikas Dubey / Himanshu Khandelia /
Abstract: The gastric proton pump (H,K-ATPase) transports a proton into the stomach lumen for every K ion exchanged in the opposite direction. In the lumen-facing state of the pump (E2), the pump selectively ...The gastric proton pump (H,K-ATPase) transports a proton into the stomach lumen for every K ion exchanged in the opposite direction. In the lumen-facing state of the pump (E2), the pump selectively binds K despite the presence of a 10-fold higher concentration of Na. The molecular basis for the ion selectivity of the pump is unknown. Using molecular dynamics simulations, free energy calculations, and Na and K-dependent ATPase activity assays, we demonstrate that the K selectivity of the pump depends upon the simultaneous protonation of the acidic residues E343 and E795 in the ion-binding site. We also show that when E936 is protonated, the pump becomes Na sensitive. The protonation-mimetic mutant E936Q exhibits weak Na-activated ATPase activity. A 2.5-Å resolution cryo-EM structure of the E936Q mutant in the K-occluded E2-Pi form shows, however, no significant structural difference compared with wildtype except less-than-ideal coordination of K in the mutant. The selectivity toward a specific ion correlates with a more rigid and less fluctuating ion-binding site. Despite being exposed to a pH of 1, the fundamental principle driving the K ion selectivity of H,K-ATPase is similar to that of Na,K-ATPase: the ionization states of the acidic residues in the ion-binding sites determine ion selectivity. Unlike the Na,K-ATPase, however, protonation of an ion-binding glutamate residue (E936) confers Na sensitivity.
History
DepositionSep 7, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_37391.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 420 pix.
= 348.6 Å
0.83 Å/pix.
x 420 pix.
= 348.6 Å
0.83 Å/pix.
x 420 pix.
= 348.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.84
Minimum - Maximum-3.5078642 - 6.032925
Average (Standard dev.)-0.0018932342 (±0.089411005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37391_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_37391_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_37391_half_map_2.map
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Sample components

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Entire : alpha-beta complex of the gastric proton pump

EntireName: alpha-beta complex of the gastric proton pump
Components
  • Complex: alpha-beta complex of the gastric proton pump
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha
    • Protein or peptide: Potassium-transporting ATPase subunit beta
  • Ligand: POTASSIUM IONPotassium
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: alpha-beta complex of the gastric proton pump

SupramoleculeName: alpha-beta complex of the gastric proton pump / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 135 KDa

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Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 114.282594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GKAENYELYQ VELGPGPSGD MAAKMSKKKA GRGGGKRKEK LENMKKEMEI NDHQLSVAEL EQKYQTSATK GLSASLAAEL LLRDGPNAL RPPRGTPEYV KFARQLAGGL QCLMWVAAAI CLIAFAIQAS EGDLTTDDNL YLALALIAVV VVTGCFGYYQ E FKSTNIIA ...String:
GKAENYELYQ VELGPGPSGD MAAKMSKKKA GRGGGKRKEK LENMKKEMEI NDHQLSVAEL EQKYQTSATK GLSASLAAEL LLRDGPNAL RPPRGTPEYV KFARQLAGGL QCLMWVAAAI CLIAFAIQAS EGDLTTDDNL YLALALIAVV VVTGCFGYYQ E FKSTNIIA SFKNLVPQQA TVIRDGDKFQ INADQLVVGD LVEMKGGDRV PADIRILQAQ GCKVDNSSLT GESEPQTRSP EC THESPLE TRNIAFFSTM CLEGTAQGLV VNTGDRTIIG RIASLASGVE NEKTPIAIEI EHFVDIIAGL AILFGATFFI VAM CIGYTF LRAMVFFMAI VVAYVPEGLL ATVTVCLSLT AKRLASKNCV VKNLEAVETL GSTSVICSDK TGTLTQNRMT VSHL WFDNH IHSADTTEDQ SGQTFDQSSE TWRALCRVLT LCNRAAFKSG QDAVPVPKRI VIGDASETAL LKFSELTLGN AMGYR ERFP KVCEIPFNST NKFQLSIHTL EDPRDPRHVL VMKGAPERVL ERCSSILIKG QELPLDEQWR EAFQTAYLSL GGLGER VLG FCQLYLSEKD YPPGYAFDVE AMNFPTSGLC FAGLVSMIDP PRATVPDAVL KCRTAGIRVI MVTGDHPITA KAIAASV GI ISEGSETVED IAARLRVPVD QVNRKDARAC VINGMQLKDM DPSELVEALR THPEMVFART SPQQKLVIVE SCQRLGAI V AVTGDGVNDS PALKKADIGV AMGIAGSDAA KNAADMILLD DNFASIVTGV EQGRLIFDNL KKSIAYTLTK NIPELTPWL IYITVSVPLP LGCITILFIE LCTDIFPSVS LAYEKAESDI MHLRPRNPKR DRLVNEPLAA YSYFQIGAIQ SFAGFTDYFT AMAQEGWFP LLCVGLRPQW ENHHLQDLQD SYGQEWTFGQ RLYQQYTCYT VFFISIQMCQ IADVLIRKTR RLSAFQQGFF R NRILVIAI VFQVCIGCFL CYCPGMPNIF NFMPIRFQWW LVPMPFSLLI FVYDEIRKLG VRCCPGSWWD QELYY

UniProtKB: Sodium/potassium-transporting ATPase subunit alpha

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Macromolecule #2: Potassium-transporting ATPase subunit beta

MacromoleculeName: Potassium-transporting ATPase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 33.113844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAALQEKKSC SQRMEEFQRY CWNPDTGQML GRTLSRWVWI SLYYVAFYVV MSGIFALCIY VLMRTIDPYT PDYQDQLKSP GVTLRPDVY GEKGLDISYN VSDSTTWAGL AHTLHRFLAG YSPAAQEGSI NCTSEKYFFQ ESFLAPNHTK FSCKFTADML Q NCSGRPDP ...String:
MAALQEKKSC SQRMEEFQRY CWNPDTGQML GRTLSRWVWI SLYYVAFYVV MSGIFALCIY VLMRTIDPYT PDYQDQLKSP GVTLRPDVY GEKGLDISYN VSDSTTWAGL AHTLHRFLAG YSPAAQEGSI NCTSEKYFFQ ESFLAPNHTK FSCKFTADML Q NCSGRPDP TFGFAEGKPC FIIKMNRIVK FLPGNSTAPR VDCAFLDQPR DGPPLQVEYF PANGTYSLHY FPYYGKKAQP HY SNPLVAA KLLNVPRNRD VVIVCKILAE HVSFDNPHDP YEGKVEFKLK IQK

UniProtKB: Potassium-transporting ATPase subunit beta

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #7: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302608
FSC plot (resolution estimation)

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