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- PDB-6jxj: Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp) -

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Basic information

Entry
Database: PDB / ID: 6jxj
TitleRb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp)
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 sodium ion homeostasis / potassium ion import across plasma membrane / intracellular potassium ion homeostasis ...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 / intracellular potassium ion homeostasis / 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 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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / P-type ATPase, cytoplasmic domain N / HAD superfamily/HAD-like / P-type ATPase actuator domain / 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
TETRAFLUOROALUMINATE ION / O-DODECANYL OCTAETHYLENE GLYCOL / CHOLESTEROL / 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: 2.5 Å
AuthorsAbe, K. / Irie, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)148,41624
Polymers142,2032
Non-polymers6,21222
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-106 kcal/mol
Surface area53730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.230, 103.230, 369.440
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: 109220.711 Da / Num. of mol.: 1 / Mutation: R220C, S593C, Y799W, G1005S
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.: 1 / Mutation: R220C, S593C, Y799W, G1005S
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, 6 molecules

#9: 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.: 6 / 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 , 7 types, 387 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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.: 4 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT


Mass: 538.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O9
#6: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#7: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Rb
#8: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% glycerol, 20% PEG2000MME, 0.4 M RbCl, 3% 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: May 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 61014 / % possible obs: 76 % / Redundancy: 8 % / Biso Wilson estimate: 48.43 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.64
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 0.77 / Num. unique obs: 61013 / CC1/2: 0.6

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Processing

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

5ylu


Resolution: 2.5→49.71 Å / SU ML: 0.364 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3055 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2731 3198 5.24 %
Rwork0.2144 57816 -
obs0.2175 61014 76.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9763 0 364 371 10498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009310349
X-RAY DIFFRACTIONf_angle_d1.211914031
X-RAY DIFFRACTIONf_chiral_restr0.07221584
X-RAY DIFFRACTIONf_plane_restr0.00691779
X-RAY DIFFRACTIONf_dihedral_angle_d22.66913907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.4327340.3233549X-RAY DIFFRACTION17.09
2.54-2.580.449370.3222648X-RAY DIFFRACTION19.92
2.58-2.620.335260.3265792X-RAY DIFFRACTION24.36
2.62-2.660.3201560.3238942X-RAY DIFFRACTION28.85
2.66-2.710.3132520.34121100X-RAY DIFFRACTION33.19
2.71-2.760.3454640.32411316X-RAY DIFFRACTION40.67
2.76-2.820.3733840.32311579X-RAY DIFFRACTION48.19
2.82-2.880.3581920.30941916X-RAY DIFFRACTION57.6
2.88-2.950.32491330.29772477X-RAY DIFFRACTION75.98
2.95-3.020.35471870.28793164X-RAY DIFFRACTION96.74
3.02-3.110.33842030.27833225X-RAY DIFFRACTION99.83
3.11-3.20.33871930.26433271X-RAY DIFFRACTION99.74
3.2-3.30.34691790.25353270X-RAY DIFFRACTION99.83
3.3-3.420.31041780.23173293X-RAY DIFFRACTION99.94
3.42-3.550.31391860.22343302X-RAY DIFFRACTION99.77
3.55-3.720.25691910.20763286X-RAY DIFFRACTION99.91
3.72-3.910.29261500.18533324X-RAY DIFFRACTION99.8
3.91-4.160.25691870.17623321X-RAY DIFFRACTION99.97
4.16-4.480.20521830.15693364X-RAY DIFFRACTION99.94
4.48-4.930.22371850.15013329X-RAY DIFFRACTION99.97
4.93-5.640.2431760.1793375X-RAY DIFFRACTION99.92
5.64-7.10.26352120.22133386X-RAY DIFFRACTION100
7.1-49.720.22132100.20873587X-RAY DIFFRACTION99.61
Refinement TLS params.Method: refined / Origin x: 34.7785 Å / Origin y: -33.2659 Å / Origin z: -41.184 Å
111213212223313233
T0.2284 Å2-0.0844 Å20.0538 Å2-0.1778 Å2-0.0336 Å2--0.2446 Å2
L0.1413 °20.0056 °20.2826 °2-0.2874 °20.2444 °2--1.4719 °2
S0.041 Å °0.063 Å °0.0437 Å °0.0825 Å °-0.0093 Å °0.0791 Å °0.0819 Å °-0.0764 Å °-0.0248 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA47 - 1033
2X-RAY DIFFRACTION1allB29 - 290
3X-RAY DIFFRACTION1allA1101 - 1114
4X-RAY DIFFRACTION1allB301 - 308
5X-RAY DIFFRACTION1allA1201 - 1489
6X-RAY DIFFRACTION1allB401 - 482

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