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- PDB-6jxk: Rb+-bound E2-MgF state of the gastric proton pump (Wild-type) -

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Basic information

Entry
Database: PDB / ID: 6jxk
TitleRb+-bound E2-MgF state of the gastric proton pump (Wild-type)
Components(Potassium-transporting ATPase ...) x 2
KeywordsMEMBRANE PROTEIN / P-type ATPase / proton pump / gastric / ion pump
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 / ATPase activator activity / potassium ion binding / 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 / 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 / Cation-transporting P-type ATPase, C-terminal ...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 / haloacid dehalogenase-like hydrolase / 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
CHOLESTEROL / : / TETRAFLUOROMAGNESATE(2-) / 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: 4.3 Å
AuthorsAbe, K. / Irie, K. / Yamamoto, K.
CitationJournal: Elife / Year: 2019
Title: A single K + -binding site in the crystal structure of the gastric proton pump.
Authors: Yamamoto, K. / Dubey, V. / Irie, K. / Nakanishi, H. / Khandelia, H. / Fujiyoshi, Y. / Abe, K.
History
DepositionApr 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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_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 / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 30, 2020Group: Database references / Structure summary / Category: chem_comp / citation / Item: _chem_comp.pdbx_synonyms / _citation.title
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
F: Potassium-transporting ATPase subunit beta
E: Potassium-transporting ATPase alpha chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,38724
Polymers284,3614
Non-polymers3,02720
Water0
1
A: Potassium-transporting ATPase alpha chain 1
B: Potassium-transporting ATPase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,25110
Polymers142,1802
Non-polymers1,0718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-20 kcal/mol
Surface area54660 Å2
MethodPISA
2
F: Potassium-transporting ATPase subunit beta
E: Potassium-transporting ATPase alpha chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,13614
Polymers142,1802
Non-polymers1,95612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-6 kcal/mol
Surface area54970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.510, 106.430, 250.960
Angle α, β, γ (deg.)90.000, 107.790, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Potassium-transporting ATPase ... , 2 types, 4 molecules AEBF

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


Mass: 109197.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP4A / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnT1- / 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP4B / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnT1- / References: UniProt: P18434

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Sugars , 1 types, 8 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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 , 4 types, 12 molecules

#3: Chemical ChemComp-MF4 / TETRAFLUOROMAGNESATE(2-) / MAGNESIUMTETRAFLUORIDE


Mass: 100.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F4Mg
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K

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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: 4.36 Å3/Da / Density % sol: 71.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% glycerol, 15% PEG6000, 0.1M CH3COOK, 6% methylpentanediol, 5 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.3→48 Å / Num. obs: 31390 / % possible obs: 94.94 % / Redundancy: 6.6 % / Biso Wilson estimate: 158.44 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.19
Reflection shellResolution: 4.3→4.5 Å / Mean I/σ(I) obs: 0.92 / CC1/2: 0.75 / % possible all: 53.46

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ylu

5ylu


Resolution: 4.3→47.79 Å / SU ML: 0.7173 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.8419
RfactorNum. reflection% reflection
Rfree0.3384 1546 4.93 %
Rwork0.2627 --
obs0.2666 31390 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 244.02 Å2
Refinement stepCycle: LAST / Resolution: 4.3→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19623 0 186 0 19809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004220273
X-RAY DIFFRACTIONf_angle_d0.980827586
X-RAY DIFFRACTIONf_chiral_restr0.05383147
X-RAY DIFFRACTIONf_plane_restr0.0073543
X-RAY DIFFRACTIONf_dihedral_angle_d22.44397452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.440.436680.33891438X-RAY DIFFRACTION50.59
4.44-4.60.37951370.32782732X-RAY DIFFRACTION96.6
4.6-4.780.37151510.30482853X-RAY DIFFRACTION99.77
4.78-50.3261190.28582849X-RAY DIFFRACTION99.93
5-5.260.33611510.27872809X-RAY DIFFRACTION99.8
5.26-5.590.38051730.27982812X-RAY DIFFRACTION99.63
5.59-6.020.351450.26282846X-RAY DIFFRACTION99.83
6.02-6.630.34011310.26982877X-RAY DIFFRACTION99.97
6.63-7.580.32161500.25642838X-RAY DIFFRACTION99.83
7.58-9.540.32521660.24132858X-RAY DIFFRACTION99.93
9.54-47.790.32271550.23722932X-RAY DIFFRACTION98.94
Refinement TLS params.Method: refined / Origin x: 217.7477 Å / Origin y: -32.2571 Å / Origin z: 56.926 Å
111213212223313233
T0.5286 Å20.1481 Å2-0.0181 Å2-0.8586 Å20.1196 Å2--0.4804 Å2
L0.2944 °20.1906 °20.2255 °2-0.4306 °2-0.109 °2--0.6145 °2
S-0.0009 Å °0.5038 Å °-0.1905 Å °-0.0146 Å °0.0015 Å °-0.0215 Å °-0.0665 Å °0.0143 Å °0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA47 - 1033
2X-RAY DIFFRACTION1allB20 - 290
3X-RAY DIFFRACTION1allF25 - 290
4X-RAY DIFFRACTION1allE47 - 1033
5X-RAY DIFFRACTION1allA1101 - 1106
6X-RAY DIFFRACTION1allB301 - 302
7X-RAY DIFFRACTION1allF301 - 307
8X-RAY DIFFRACTION1allE1101 - 1105

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