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- PDB-5ylv: Crystal structure of the gastric proton pump complexed with SCH28080 -

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Basic information

Entry
Database: PDB / ID: 5ylv
TitleCrystal structure of the gastric proton pump complexed with SCH28080
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 sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding ...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 sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / intracellular potassium ion homeostasis / 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 and potassium ATPases beta subunits signature 2. / 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 and potassium ATPases beta subunits signature 2. / 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. / : / 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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / HAD superfamily/HAD-like / 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 / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8WX / O-DODECANYL OCTAETHYLENE GLYCOL / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / RUBIDIUM ION / 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: 2.79977781895 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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)150,52613
Polymers147,4392
Non-polymers3,08611
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-52 kcal/mol
Surface area53250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.050, 105.050, 368.540
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
Details: Chain A is N-terminal deletion mutant starting Met49 and its N-terminus has TEV protease site. Cleavaged by TEV protease, glycine residue is left in front of Met49.
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


Mass: 32982.652 Da / Num. of mol.: 1 / Fragment: UNP residues 2-290
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: 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

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Non-polymers , 6 types, 37 molecules

#3: Chemical ChemComp-8WX / 2-(2-methyl-8-phenylmethoxy-imidazo[1,2-a]pyridin-3-yl)ethanenitrile


Mass: 277.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3O
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 538.755 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O9
#6: Chemical ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Rb
#8: 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.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% glycerol, 20% PEG2000MME, 0.2M RbCl, 5% tert-butanol, 5mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.3 Å / Num. obs: 59284 / % possible obs: 92.27 % / Redundancy: 7.8 % / Biso Wilson estimate: 73.9593491835 Å2 / Net I/σ(I): 9.88
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.35 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2368 / Rpim(I) all: 0.86 / % possible all: 40.65

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Processing

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

5ylu


Resolution: 2.79977781895→48.2956647824 Å / SU ML: 0.455159549979 / Cross valid method: FREE R-VALUE / σ(F): 1.34545459227 / Phase error: 32.9956430138
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.292091713448 2746 5.01634971959 %
Rwork0.239649552158 51995 -
obs0.242277654791 54741 92.2637407089 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.8135855892 Å2
Refinement stepCycle: LAST / Resolution: 2.79977781895→48.2956647824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9739 0 169 29 9937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010156455510410134
X-RAY DIFFRACTIONf_angle_d1.2611091412713755
X-RAY DIFFRACTIONf_chiral_restr0.1194922684591552
X-RAY DIFFRACTIONf_plane_restr0.007970062189241761
X-RAY DIFFRACTIONf_dihedral_angle_d21.2221811323751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7998-2.8480.503856727917550.471464110315937X-RAY DIFFRACTION33.7529772031
2.848-2.89980.469431327566770.3854654155341284X-RAY DIFFRACTION47.3391304348
2.8998-2.95560.476029209488780.3504361977821827X-RAY DIFFRACTION65.1282051282
2.9556-3.01590.3601048216831370.3253964159492731X-RAY DIFFRACTION97.5842123171
3.0159-3.08150.3855244269481360.3178267101222774X-RAY DIFFRACTION100
3.0815-3.15320.307454023221450.3050692072512760X-RAY DIFFRACTION99.9655884377
3.1532-3.2320.3507133163941650.2949425140582779X-RAY DIFFRACTION99.9660441426
3.232-3.31940.3433743405851630.2761070468032752X-RAY DIFFRACTION100
3.3194-3.4170.3135410573571600.282174948372786X-RAY DIFFRACTION100
3.417-3.52730.3221732151591230.2622881045192824X-RAY DIFFRACTION100
3.5273-3.65330.3124572749121360.252404508362809X-RAY DIFFRACTION99.9660556687
3.6533-3.79950.3365975375271620.2483245320832773X-RAY DIFFRACTION99.8978897209
3.7995-3.97240.3382614404681390.2326467423322810X-RAY DIFFRACTION100
3.9724-4.18170.3008804785171560.2275114324492808X-RAY DIFFRACTION100
4.1817-4.44350.2666722069061460.2138537649332819X-RAY DIFFRACTION99.9662845583
4.4435-4.78630.2648837436461370.1948548819962873X-RAY DIFFRACTION100
4.7863-5.26740.239883039371530.1946926054612834X-RAY DIFFRACTION100
5.2674-6.02840.2806308115611460.2253777855892863X-RAY DIFFRACTION99.9335768848
6.0284-7.59040.2799711361491660.2327650947012906X-RAY DIFFRACTION99.8050682261
7.5904-48.30280.2398402209251660.2232092365043046X-RAY DIFFRACTION99.5043370508

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