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- EMDB-61331: P5A-ATPase ATP13A1 in E2P state -

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Basic information

Entry
Database: EMDB / ID: EMD-61331
TitleP5A-ATPase ATP13A1 in E2P state
Map dataPostprocessed by DeepEMhancer
Sample
  • Complex: ATP13A1 in E2P state
    • Protein or peptide: Endoplasmic reticulum transmembrane helix translocase
KeywordsER membrane / Transmembrane helices / Translocation / E2P 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: 3.67 Å
AuthorsLi Y / Liao J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2025
Title: ATP13A1 engages SEC61 to facilitate substrate-specific translocation.
Authors: Xiaoyan Yang / Yi Li / Chengxi Yang / Tingting Li / Zhiyu Fang / Zhigang Feng / Jun Liao / Yan Zou /
Abstract: The accurate targeting of proteins to their designated cellular compartments is essential for maintaining proper cellular architecture and function. However, interpreting and sorting the highly ...The accurate targeting of proteins to their designated cellular compartments is essential for maintaining proper cellular architecture and function. However, interpreting and sorting the highly variable targeting sequences in secreted and membrane proteins present a substantial challenge for achieving precise localization within the secretory pathway. In this study, we demonstrate that atypical signal sequences, characterized by high hydrophobicity and/or the absence of characteristic charges, are recognized by the signal recognition particle and targeted to the endoplasmic reticulum in a reverse orientation. These misoriented signal sequences are subsequently dislocated by the P5A-ATPase ATP13A1 and delivered to SEC61 for further translocation. Using cryo-electron microscopy, we determined the structures of human ATP13A1 in multiple conformations (3.40- to 3.87-angstrom resolution), revealing key residues within its substrate-binding pocket that engage signal sequences through polar interactions. Collectively, our findings elucidate a comprehensive, substrate-specific translocation pathway that ensures both high efficiency and fidelity in protein subcellular localization.
History
DepositionAug 27, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61331.png

Downloads & links

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Map

FileDownload / File: emd_61331.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed by DeepEMhancer
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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.001815615 - 2.04382
Average (Standard dev.)0.0029735812 (±0.03853605)
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_61331_additional_1.map
AnnotationConsensus map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half-A map

Fileemd_61331_half_map_1.map
AnnotationHalf-A map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-B map

Fileemd_61331_half_map_2.map
AnnotationHalf-B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ATP13A1 in E2P state

EntireName: ATP13A1 in E2P state
Components
  • Complex: ATP13A1 in E2P state
    • Protein or peptide: Endoplasmic reticulum transmembrane helix translocase

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Supramolecule #1: ATP13A1 in E2P state

SupramoleculeName: ATP13A1 in E2P 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: 133.105375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAAVGNA VPCGARPCGV RPDGQPKPGP QPRALLAAGP ALIANGDELV AAVWPYRRLA LLRRLTVLPF AGLLYPAWLG AAAAGCWGW GSSWVQIPEA ALLVLATICL AHALTVLSGH WSVHAHCALT CTPEYDPSKA TFVKVVPTPN NGSTELVALH R NEGEDGLE ...String:
MAAAAAVGNA VPCGARPCGV RPDGQPKPGP QPRALLAAGP ALIANGDELV AAVWPYRRLA LLRRLTVLPF AGLLYPAWLG AAAAGCWGW GSSWVQIPEA ALLVLATICL AHALTVLSGH WSVHAHCALT CTPEYDPSKA TFVKVVPTPN NGSTELVALH R NEGEDGLE VLSFEFQKIK YSYDALEKKQ FLPVAFPVGN AFSYYQSNRG FQEDSEIRAA EKKFGSNKAE MVVPDFSELF KE RATAPFF VFQVFCVGLW CLDEYWYYSV FTLSMLVAFE ASLVQQQMRN MSEIRKMGNK PHMIQVYRSR KWRPIASDEI VPG DIVSIG RSPQENLVPC DVLLLRGRCI VDEAMLTGES VPQMKEPIED LSPDRVLDLQ ADSRLHVIFG GTKVVQHIPP QKAT TGLKP VDSGCVAYVL RTGFNTSQGK LLRTILFGVK RVTANNLETF IFILFLLVFA IAAAAYVWIE GTKDPSRNRY KLFLE CTLI LTSVVPPELP IELSLAVNTS LIALAKLYMY CTEPFRIPFA GKVEVCCFDK TGTLTSDSLV VRGVAGLRDG KEVTPV SSI PVETHRALAS CHSLMQLDDG TLVGDPLEKA MLTAVDWTLT KDEKVFPRSI KTQGLKIHQR FHFASALKRM SVLASYE KL GSTDLCYIAA VKGAPETLHS MFSQCPPDYH HIHTEISREG ARVLALGYKE LGHLTHQQAR EVKREALECS LKFVGFIV V SCPLKADSKA VIREIQNASH RVVMITGDNP LTACHVAQEL HFIEKAHTLI LQPPSEKGRQ CEWRSIDGSI VLPLARGSP KALALEYALC LTGDGLAHLQ ATDPQQLLRL IPHVQVFARV APKQKEFVIT SLKELGYVTL MCGDGTNDVG ALKHADVGVA LLANAPERV VERRRRPRDS PTLSNSGIRA TSRTAKQRSG LPPSEEQPTS QRDRLSQVLR DLEDESTPIV KLGDASIAAP F TSKLSSIQ CICHVIKQGR CTLVTTLQMF KILALNALIL AYSQSVLYLE GVKFSDFQAT LQGLLLAGCF LFISRSKPLK TL SRERPLP NIFNLYTILT VMLQFFVHFL SLVYLYREAQ ARSPEKQEQF VDLYKEFEPS LVNSTVYIMA MAMQMATFAI NYK GPPFME SLPENKPLVW SLAVSLLAII GLLLGSSPDF NSQFGLVDIP VEFKLVIAQV LLLDFCLALL ADRVLQFFLG TPKL KVPS

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

MicroscopeFEI TITAN 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: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201585
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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