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- EMDB-61329: P5A-ATPase ATP13A1 in E1P state -

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Basic information

Entry
Database: EMDB / ID: EMD-61329
TitleP5A-ATPase ATP13A1 in E1P state
Map dataConsensus map
Sample
  • Complex: ATP13A1 in E1P state
    • Protein or peptide: Endoplasmic reticulum transmembrane helix translocase
KeywordsER membrane / Transmembrane helices / Translocation / E1P state / MEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type manganese transporter activity / extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / P-type ion transporter activity / ATPase-coupled monoatomic cation transmembrane transporter activity / Ion transport by P-type ATPases / transmembrane transport / intracellular calcium ion homeostasis / protein transport ...ABC-type manganese transporter activity / extraction of mislocalized protein from ER membrane / membrane protein dislocase activity / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / P-type ion transporter activity / ATPase-coupled monoatomic cation transmembrane transporter activity / Ion transport by P-type ATPases / transmembrane transport / intracellular calcium ion homeostasis / protein transport / monoatomic ion transmembrane transport / endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / metal ion binding / membrane
Similarity search - Function
: / P5A-ATPase, transmembrane helical hairpin / P-type ATPase, subfamily V / 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 ...: / P5A-ATPase, transmembrane helical hairpin / P-type ATPase, subfamily V / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsLi Y / Liao J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: ATP13A1 engages GET3 to facilitate substrate-specific translocation
Authors: Yang X / Li Y / Li T / Fang Z / Feng Z / Liao J / Zou Y
History
DepositionAug 27, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61329.png

Downloads & links

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Map

FileDownload / File: emd_61329.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 240 pix.
= 199.68 Å		0.83 Å/pix.
x 240 pix.
= 199.68 Å		0.83 Å/pix.
x 240 pix.
= 199.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.049
Minimum - Maximum-0.0017016442 - 2.0940652
Average (Standard dev.)0.0028198624 (±0.038105343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 199.68001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus map

Fileemd_61329_additional_1.map
AnnotationConsensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus map

Fileemd_61329_half_map_1.map
AnnotationConsensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus map

Fileemd_61329_half_map_2.map
AnnotationConsensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATP13A1 in E1P state

EntireName: ATP13A1 in E1P state
Components
  • Complex: ATP13A1 in E1P state
    • Protein or peptide: Endoplasmic reticulum transmembrane helix translocase

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Supramolecule #1: ATP13A1 in E1P state

SupramoleculeName: ATP13A1 in E1P state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: ATP13A1 purified in BeF3- buffer
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Endoplasmic reticulum transmembrane helix translocase

MacromoleculeName: Endoplasmic reticulum transmembrane helix translocase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.30432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHWSVHAHCA LTCTPEYDPS KATFVKVVPT PNNGSTELVA LHRNEGEDGL EVLSFEFQKI KYSYDALEKK QFLPVAFPVG NAFSYYQSN RGFQEDSEIR AAEKKFGSNK AEMVVPDFSE LFKERATAPF FVFQVFCVGL WCLDEYWYYS VFTLSMLVAF E ASLVQQQM ...String:
GHWSVHAHCA LTCTPEYDPS KATFVKVVPT PNNGSTELVA LHRNEGEDGL EVLSFEFQKI KYSYDALEKK QFLPVAFPVG NAFSYYQSN RGFQEDSEIR AAEKKFGSNK AEMVVPDFSE LFKERATAPF FVFQVFCVGL WCLDEYWYYS VFTLSMLVAF E ASLVQQQM RNMSEIRKMG NKPHMIQVYR SRKWRPIASD EIVPGDIVSI GRSPQENLVP CDVLLLRGRC IVDEAMLTGE SV PQMKEPI EDLSPDRVLD LQADSRLHVI FGGTKVVQHI PPQKATTGLK PVDSGCVAYV LRTGFNTSQG KLLRTILFGV KRV TANNLE TFIFILFLLV FAIAAAAYVW IEGTKDPSRN RYKLFLECTL ILTSVVPPEL PIELSLAVNT SLIALAKLYM YCTE PFRIP FAGKVEVCCF DKTGTLTSDS LVVRGVAGLR DGKEVTPVSS IPVETHRALA SCHSLMQLDD GTLVGDPLEK AMLTA VDWT LTKDEKVFPR SIKTQGLKIH QRFHFASALK RMSVLASYEK LGSTDLCYIA AVKGAPETLH SMFSQCPPDY HHIHTE ISR EGARVLALGY KELGHLTHQQ AREVKREALE CSLKFVGFIV VSCPLKADSK AVIREIQNAS HRVVMITGDN PLTACHV AQ ELHFIEKAHT LILQPPSEKG RQCEWRSIDG SIVLPLARGS PKALALEYAL CLTGDGLAHL QATDPQQLLR LIPHVQVF A RVAPKQKEFV ITSLKELGYV TLMCGDGTND VGALKHADVG VALLANAPER VVERRRRPRD SPTLSNSGIR ATSRTAKQR SGLPPSEEQP TSQRDRLSQV LRDLEDESTP IVKLGDASIA APFTSKLSSI QCICHVIKQG RCTLVTTLQM FKILALNALI LAYSQSVLY LEGVKFSDFQ ATLQGLLLAG CFLFISRSKP LKTLSRERPL PNIFNLYTIL TVMLQFFVHF LSLVYLYREA Q ARSPEKQE QFVDLYKEFE PSLVNSTVYI MAMAMQMATF AINYKGPPFM ESLPENKPLV WSLAVSLLAI IGLLLGSSPD FN SQFGLVD IPVEFKLVIA QVLLLDFCLA LLADRVLQFF LG

UniProtKB: Endoplasmic reticulum transmembrane helix translocase

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClSodium chloride
5.0 mMMgCl2Magnesium chloride
0.006 %GDNGlyco-diosgenin
2.0 mMBeSO4Beryllium sulfate
10.0 mMNaFSodium fluoride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7365 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER / Details: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157126
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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