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- EMDB-22264: Structure of P5A-ATPase Spf1, endogenous substrate-bound -

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Basic information

Entry
Database: EMDB / ID: EMD-22264
TitleStructure of P5A-ATPase Spf1, endogenous substrate-bound
Map dataunsharpened, lowpass-filtered map
Sample
  • Complex: P5A-ATPase Spf1, endogenous substrate bound
    • Protein or peptide: P5A-type ATPase
    • Protein or peptide: Putative endogenous substrate transmembrane helix
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
KeywordsP-type ATPase / transmembrane helix dislocase / protein quality control / endoplasmic reticulum / TRANSPORT PROTEIN
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 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Endoplasmic reticulum transmembrane helix translocase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPark E / Sim SI
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xmu
  • Surface level: 0.21
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22264.png

Downloads & links

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Map

FileDownload / File: emd_22264.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened, lowpass-filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 256 pix.
= 304.64 Å		1.19 Å/pix.
x 256 pix.
= 304.64 Å		1.19 Å/pix.
x 256 pix.
= 304.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21 / Movie #1: 0.21
Minimum - Maximum-0.4190229 - 1.1832993
Average (Standard dev.)0.0017757028 (±0.02991919)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.191.191.19
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z304.640304.640304.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.4191.1830.002

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Supplemental data

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Mask #1

Fileemd_22264_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_22264_additional.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: P5A-ATPase Spf1, endogenous substrate-bound

Fileemd_22264_half_map_1.map
AnnotationP5A-ATPase Spf1, endogenous substrate-bound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: P5A-ATPase Spf1, endogenous substrate-bound

Fileemd_22264_half_map_2.map
AnnotationP5A-ATPase Spf1, endogenous substrate-bound
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : P5A-ATPase Spf1, endogenous substrate bound

EntireName: P5A-ATPase Spf1, endogenous substrate bound
Components
  • Complex: P5A-ATPase Spf1, endogenous substrate bound
    • Protein or peptide: P5A-type ATPase
    • Protein or peptide: Putative endogenous substrate transmembrane helix
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: P5A-ATPase Spf1, endogenous substrate bound

SupramoleculeName: P5A-ATPase Spf1, endogenous substrate bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: P5A-type ATPase

MacromoleculeName: P5A-type ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 137.573156 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MTKKSFVSSP IVRDSTLLVP KSLIAKPYVL PFFPLYATFA QLYFQQYDRY IKGPEWTFVY LGTLVSLNIL VMLMPAWNVK IKAKFNYST TKNVNEATHI LIYTTPNNGS DGIVEIQRVT EAGSLQTFFQ FQKKRFLWHE NEQVFSSPKF LVDESPKIGD F QKCKGHSG ...String:
MTKKSFVSSP IVRDSTLLVP KSLIAKPYVL PFFPLYATFA QLYFQQYDRY IKGPEWTFVY LGTLVSLNIL VMLMPAWNVK IKAKFNYST TKNVNEATHI LIYTTPNNGS DGIVEIQRVT EAGSLQTFFQ FQKKRFLWHE NEQVFSSPKF LVDESPKIGD F QKCKGHSG DLTHLKRLYG ENSFDIPIPT FMELFKEHAV APLFVFQVFC VALWLLDEFW YYSLFNLFMI ISMEAAAVFQ RL TALKEFR TMGIKPYTIN VFRNKKWVAL QTNELLPMDL VSITRTAEES AIPCDLILLD GSAIVNEAML SGESTPLLKE SIK LRPSED NLQLDGVDKI AVLHGGTKAL QVTPPEHKSD IPPPPDGGAL AIVTKTGFET SQGSLVRVMI YSAERVSVDN KEAL MFILF LLIFAVIASW YVWVEGTKMG RIQSKLILDC ILIITSVVPP ELPMELTMAV NSSLAALAKF YVYCTEPFRI PFAGR IDVC CFDKTGTLTG EDLVFEGLAG ISADSENIRH LYSAAEAPES TILVIGAAHA LVKLEDGDIV GDPMEKATLK AVGWAV ERK NSNYREGTGK LDIIRRFQFS SALKRSASIA SHNDALFAAV KGAPETIRER LSDIPKNYDE IYKSFTRSGS RVLALAS KS LPKMSQSKID DLNRDDVESE LTFNGFLIFH CPLKDDAIET IKMLNESSHR SIMITGDNPL TAVHVAKEVG IVFGETLI L DRAGKSDDNQ LLFRDVEETV SIPFDPSKDT FDHSKLFDRY DIAVTGYALN ALEGHSQLRD LLRHTWVYAR VSPSQKEFL LNTLKDMGYQ TLMCGDGTND VGALKQAHVG IALLNGTEEG LKKLGEQRRL EGMKMMYIKQ TEFMARWNQP QPPVPEPIAH LFPPGPKNP HYLKALESKG TVITPEIRKA VEEANSKPVE VIKPNGLSEK KPADLASLLL NSAGDAQGDE APALKLGDAS C AAPFTSKL ANVSAVTNII RQGRCALVNT IQMYKILALN CLISAYSLSI IYMAGVKFGD GQATVSGLLL SVCFLSISRG KP LEKLSKQ RPQSGIFNVY IMGSILSQFA VHIATLVYIT TEIYKLEPRE PQVDLEKEFA PSLLNTGIFI IQLVQQVSTF AVN YQGEPF RENIRSNKGM YYGLLGVTGL ALASATEFLP ELNEAMKFVP MTDDFKIKLT LTLLLDFFGS WGVEHFFKFF FMDD KPSDI SVQQVKIASK GATGGSTAGG ATTASGTGEN LYFQ

UniProtKB: Endoplasmic reticulum transmembrane helix translocase

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Macromolecule #2: Putative endogenous substrate transmembrane helix

MacromoleculeName: Putative endogenous substrate transmembrane helix / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 1.720111 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)

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Macromolecule #3: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 776554
Startup modelType of model: OTHER / Details: Ab initio reconstruction in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 268876
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.12.4) / Details: Non-uniform refinement in cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.12.4)
FSC plot (resolution estimation)

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