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- PDB-5ylu: Crystal structure of the gastric proton pump complexed with vonoprazan -

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Basic information

Entry
Database: PDB / ID: 5ylu
TitleCrystal structure of the gastric proton pump complexed with vonoprazan
Components(Potassium-transporting ATPase ...) x 2
KeywordsMEMBRANE PROTEIN / gastric / proton pump / H+ / K+-ATPase / P-type ATPase / transporter
Function / homology
Function and homology information


H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / 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 ...H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / 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 / potassium ion binding / ATPase activator activity / potassium ion transmembrane transport / proton transmembrane transport / cell adhesion / apical plasma membrane / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / : / Sodium / potassium ATPase beta chain ...Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / 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 / haloacid dehalogenase-like hydrolase / 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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
O-DODECANYL OCTAETHYLENE GLYCOL / Chem-HKT / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Potassium-transporting ATPase subunit beta / Potassium-transporting ATPase alpha chain 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79988962319 Å
AuthorsAbe, K. / Irie, K. / Nakanishi, H. / Fujiyoshi, Y.
CitationJournal: Nature / Year: 2018
Title: Crystal structures of the gastric proton pump
Authors: Abe, K. / Irie, K. / Nakanishi, H. / Suzuki, H. / Fujiyoshi, Y.
History
DepositionOct 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium-transporting ATPase alpha chain 1
B: Potassium-transporting ATPase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,12411
Polymers147,4392
Non-polymers3,6859
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-21 kcal/mol
Surface area53310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.820, 104.820, 367.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Potassium-transporting ATPase ... , 2 types, 2 molecules AB

#1: Protein Potassium-transporting ATPase alpha chain 1 / Gastric H(+)/K(+) ATPase subunit alpha / Proton pump


Mass: 114456.734 Da / Num. of mol.: 1 / Mutation: R220C, S593C, G1005S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP4A / Plasmid: pFB-based / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) / References: UniProt: P19156, H+/K+-exchanging ATPase
#2: Protein Potassium-transporting ATPase subunit beta / Gastric H(+)/K(+) ATPase subunit beta / Proton pump beta chain / gp60-90


Mass: 32982.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP4B / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) / References: UniProt: P18434

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Sugars , 1 types, 3 molecules

#7: 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.: 3
Source method: isolated from a genetically manipulated source
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, 43 molecules

#3: Chemical ChemComp-HKT / 1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine / Vonoprazan


Mass: 345.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16FN3O2S / Comment: medication, antibiotic*YM
#4: 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.: 2 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT


Mass: 538.755 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O9
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.25 Å3/Da / Density % sol: 71.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% glycerol, 20% PEG2000MME, 0.4M CH3COONa, 3% methylpentanediol, 5mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.18 Å / Num. obs: 58652 / % possible obs: 87.51 % / Redundancy: 5.2 % / Biso Wilson estimate: 40.6363630375 Å2 / Rmerge(I) obs: 0.1201 / Rpim(I) all: 0.05748 / Net I/σ(I): 11.04
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.689 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 31309 / Rpim(I) all: 0.7873 / % possible all: 38.17

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Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y0B

5y0b


Resolution: 2.79988962319→48.1766667 Å / SU ML: 0.424251521214 / Cross valid method: FREE R-VALUE / σ(F): 1.34782616616 / Phase error: 30.2648382541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288360075303 2610 5.06756756757 %
Rwork0.236714923457 48894 -
obs0.239318208654 51504 87.511469059 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.7477478754 Å2
Refinement stepCycle: LAST / Resolution: 2.79988962319→48.1766667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9624 0 223 37 9884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092419744410069
X-RAY DIFFRACTIONf_angle_d1.3128404183713652
X-RAY DIFFRACTIONf_chiral_restr0.08033520810311540
X-RAY DIFFRACTIONf_plane_restr0.007824042079331744
X-RAY DIFFRACTIONf_dihedral_angle_d21.69748650553759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7999-2.85080.414316787834580.3895178749451016X-RAY DIFFRACTION35.1439790576
2.8508-2.90560.433400144627590.3746216056431207X-RAY DIFFRACTION41.837409121
2.9056-2.96490.426562521061860.3337720080251430X-RAY DIFFRACTION50.3989361702
2.9649-3.02940.3869333378311040.3335355694931712X-RAY DIFFRACTION59.4435351882
3.0294-3.09980.3582308060471360.3306642762782231X-RAY DIFFRACTION77.4795417349
3.0998-3.17730.3646714417921250.3199123657532947X-RAY DIFFRACTION99.5786061588
3.1773-3.26320.3464383261531600.2988372042782880X-RAY DIFFRACTION99.5415848068
3.2632-3.35920.3333036282231330.2798814395452905X-RAY DIFFRACTION99.6392259757
3.3592-3.46760.330105165141610.2671377470232876X-RAY DIFFRACTION99.6064283372
3.4676-3.59150.308444729011660.2471027420732894X-RAY DIFFRACTION99.836867863
3.5915-3.73530.2838979492551680.2352594746622925X-RAY DIFFRACTION99.9353796446
3.7353-3.90520.2631681707591320.2226854605452939X-RAY DIFFRACTION99.7725795971
3.9052-4.1110.2859505304721740.2150282765612882X-RAY DIFFRACTION99.7063621533
4.111-4.36840.2375984303381330.2013197307572978X-RAY DIFFRACTION99.7435075345
4.3684-4.70540.296942073041460.1816475804542933X-RAY DIFFRACTION99.7408487204
4.7054-5.17850.2108328207821760.1840726030572959X-RAY DIFFRACTION99.9043977055
5.1785-5.92660.2906028644451620.205526487482988X-RAY DIFFRACTION99.8731769182
5.9266-7.46250.2275737718291710.2117460384793015X-RAY DIFFRACTION99.6247654784
7.4625-48.18380.2352747506811600.2120632985443177X-RAY DIFFRACTION99.0501632532

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