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- PDB-6xmq: Structure of P5A-ATPase Spf1, AMP-PCP-bound form -

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Basic information

Entry
Database: PDB / ID: 6xmq
TitleStructure of P5A-ATPase Spf1, AMP-PCP-bound form
ComponentsP5A-type ATPase
KeywordsTRANSPORT PROTEIN / P-type ATPase / transmembrane helix dislocase / protein quality control / endoplasmic reticulum
Function / homology
Function and homology information


extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / intracellular manganese ion homeostasis / sterol homeostasis / Ion transport by P-type ATPases / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / protein hexamerization ...extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / intracellular manganese ion homeostasis / sterol homeostasis / Ion transport by P-type ATPases / P-type ion transporter activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / ATPase-coupled monoatomic cation transmembrane transporter activity / cis-Golgi network / protein hexamerization / phosphatidylinositol-4-phosphate binding / protein unfolding / transmembrane transport / intracellular calcium ion homeostasis / protein transport / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
: / P-type ATPase, subfamily V / 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, subfamily V / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Endoplasmic reticulum transmembrane helix translocase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPark, E. / Sim, S.I.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Science / Year: 2020
Title: The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase.
Authors: Michael J McKenna / Sue Im Sim / Alban Ordureau / Lianjie Wei / J Wade Harper / Sichen Shao / Eunyong Park /
Abstract: Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A- ...Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A-adenosine triphosphatase (ATPase) transporter ATP13A1 (Spf1 in yeast) directly interacted with the transmembrane segment (TM) of mitochondrial tail-anchored proteins. P5A-ATPase activity mediated the extraction of mistargeted proteins from the endoplasmic reticulum (ER). Cryo-electron microscopy structures of Spf1 revealed a large, membrane-accessible substrate-binding pocket that alternately faced the ER lumen and cytosol and an endogenous substrate resembling an α-helical TM. Our results indicate that the P5A-ATPase could dislocate misinserted hydrophobic helices flanked by short basic segments from the ER. TM dislocation by the P5A-ATPase establishes an additional class of P-type ATPase substrates and may correct mistakes in protein targeting or topogenesis.
History
DepositionJun 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: P5A-type ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,1033
Polymers137,5731
Non-polymers5302
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1020 Å2
ΔGint-11 kcal/mol
Surface area51570 Å2

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Components

#1: Protein P5A-type ATPase


Mass: 137573.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Production host: Saccharomyces cerevisiae BY4741 (yeast)
References: UniProt: P39986, Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: P5A-ATPase Spf1 AMP-PCP-bound form / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741
Source (recombinant)Organism: Saccharomyces cerevisiae BY4741 (yeast)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 49.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
1Warp1.07particle selection
2SerialEM3.7image acquisition
4Warp1.07CTF correction
5cryoSPARC2.12.4CTF correction
12cryoSPARC2.12.4final Euler assignment
13cryoSPARC2.12.4classification
14cryoSPARC2.12.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 776554
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55920 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048597
ELECTRON MICROSCOPYf_angle_d0.54411681
ELECTRON MICROSCOPYf_dihedral_angle_d10.8545122
ELECTRON MICROSCOPYf_chiral_restr0.0411367
ELECTRON MICROSCOPYf_plane_restr0.0041469

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