[English] 日本語
Yorodumi
- EMDB-35385: Cryo-EM structure of ATP13A2 in the E1-like state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35385
TitleCryo-EM structure of ATP13A2 in the E1-like state
Map dataCryo-EM structure of ATP13A2 in the E1-like state
Sample
  • Complex: Cryo-EM structure of ATP13A2 in the E1-like state
    • Protein or peptide: Polyamine-transporting ATPase 13A2
KeywordsCryo-EM structure of ATP13A2 in the E1-like state / membrane protein / PROTEIN TRANSPORT
Function / homology
Function and homology information


polyamine transmembrane transporter activity / polyamine transmembrane transport / spermine transmembrane transport / peptidyl-aspartic acid autophosphorylation / regulation of ubiquitin-specific protease activity / ABC-type polyamine transporter activity / regulation of autophagosome size / extracellular exosome biogenesis / P-type ion transporter activity / regulation of chaperone-mediated autophagy ...polyamine transmembrane transporter activity / polyamine transmembrane transport / spermine transmembrane transport / peptidyl-aspartic acid autophosphorylation / regulation of ubiquitin-specific protease activity / ABC-type polyamine transporter activity / regulation of autophagosome size / extracellular exosome biogenesis / P-type ion transporter activity / regulation of chaperone-mediated autophagy / negative regulation of lysosomal protein catabolic process / regulation of autophagy of mitochondrion / regulation of lysosomal protein catabolic process / intracellular monoatomic cation homeostasis / autophagosome-lysosome fusion / autophagosome organization / protein localization to lysosome / phosphatidic acid binding / positive regulation of exosomal secretion / multivesicular body membrane / ATPase-coupled monoatomic cation transmembrane transporter activity / intracellular zinc ion homeostasis / regulation of protein localization to nucleus / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / cupric ion binding / regulation of mitochondrion organization / regulation of endopeptidase activity / lysosomal transport / phosphatidylinositol-3,5-bisphosphate binding / cellular response to zinc ion / regulation of intracellular protein transport / lipid homeostasis / Ion transport by P-type ATPases / autophagosome membrane / cellular response to manganese ion / regulation of macroautophagy / regulation of neuron apoptotic process / transport vesicle / autophagosome / multivesicular body / lysosomal lumen / positive regulation of protein secretion / transmembrane transport / autophagy / intracellular calcium ion homeostasis / late endosome / late endosome membrane / manganese ion binding / cellular response to oxidative stress / monoatomic ion transmembrane transport / intracellular iron ion homeostasis / vesicle / protein autophosphorylation / lysosome / neuron projection / lysosomal membrane / neuronal cell body / positive regulation of gene expression / ATP hydrolysis activity / zinc ion binding / ATP binding / membrane
Similarity search - Function
: / : / P5-type ATPase cation transporter / 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 ...: / : / P5-type ATPase cation transporter / 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
Polyamine-transporting ATPase 13A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.65 Å
AuthorsLiu ZM / Mu JQ / Xue CY
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32000850 China
CitationJournal: Nat Commun / Year: 2023
Title: Conformational cycle of human polyamine transporter ATP13A2.
Authors: Jianqiang Mu / Chenyang Xue / Lei Fu / Zongjun Yu / Minhan Nie / Mengqi Wu / Xinmeng Chen / Kun Liu / Ruiqian Bu / Ying Huang / Baisheng Yang / Jianming Han / Qianru Jiang / Kevin C Chan / ...Authors: Jianqiang Mu / Chenyang Xue / Lei Fu / Zongjun Yu / Minhan Nie / Mengqi Wu / Xinmeng Chen / Kun Liu / Ruiqian Bu / Ying Huang / Baisheng Yang / Jianming Han / Qianru Jiang / Kevin C Chan / Ruhong Zhou / Huilin Li / Ancheng Huang / Yong Wang / Zhongmin Liu /
Abstract: Dysregulation of polyamine homeostasis strongly associates with human diseases. ATP13A2, which is mutated in juvenile-onset Parkinson's disease and autosomal recessive spastic paraplegia 78, is a ...Dysregulation of polyamine homeostasis strongly associates with human diseases. ATP13A2, which is mutated in juvenile-onset Parkinson's disease and autosomal recessive spastic paraplegia 78, is a transporter with a critical role in balancing the polyamine concentration between the lysosome and the cytosol. Here, to better understand human ATP13A2-mediated polyamine transport, we use single-particle cryo-electron microscopy to solve high-resolution structures of human ATP13A2 in six intermediate states, including the putative E2 structure for the P5 subfamily of the P-type ATPases. These structures comprise a nearly complete conformational cycle spanning the polyamine transport process and capture multiple substrate binding sites distributed along the transmembrane regions, suggesting a potential polyamine transport pathway. Integration of high-resolution structures, biochemical assays, and molecular dynamics simulations allows us to obtain a better understanding of the structural basis of how hATP13A2 transports polyamines, providing a mechanistic framework for ATP13A2-related diseases.
History
DepositionFeb 15, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35385.png

Downloads & links

-
Map

FileDownload / File: emd_35385.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of ATP13A2 in the E1-like state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 328.5 Å		1.1 Å/pix.
x 300 pix.
= 328.5 Å		1.1 Å/pix.
x 300 pix.
= 328.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-1.6615261 - 2.9423249
Average (Standard dev.)0.0015604083 (±0.053667165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 328.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: The half a map of ATP13A2 in the E1-like state

Fileemd_35385_half_map_1.map
AnnotationThe half_a map of ATP13A2 in the E1-like state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: The half map of ATP13A2 in the E1-like state

Fileemd_35385_half_map_2.map
AnnotationThe half_ map of ATP13A2 in the E1-like state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of ATP13A2 in the E1-like state

EntireName: Cryo-EM structure of ATP13A2 in the E1-like state
Components
  • Complex: Cryo-EM structure of ATP13A2 in the E1-like state
    • Protein or peptide: Polyamine-transporting ATPase 13A2

-
Supramolecule #1: Cryo-EM structure of ATP13A2 in the E1-like state

SupramoleculeName: Cryo-EM structure of ATP13A2 in the E1-like state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Polyamine-transporting ATPase 13A2

MacromoleculeName: Polyamine-transporting ATPase 13A2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 124.090664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RLSGYCGSPW RVIGYHVVVW MMAGIPLLLF RWKPLWGVRL RLRPCNLAHA ETLVIEIRDK EDSSWQLFTV QVQTEAVSVG QLEPSPQSQ AEDGRSQAAV GAVPEGAWKD TAQLHKSEEA KRVLRYYLFQ GQRYIWIETQ QAFYQVSLLD HGRSCDDVHR S RHGLSLQD ...String:
RLSGYCGSPW RVIGYHVVVW MMAGIPLLLF RWKPLWGVRL RLRPCNLAHA ETLVIEIRDK EDSSWQLFTV QVQTEAVSVG QLEPSPQSQ AEDGRSQAAV GAVPEGAWKD TAQLHKSEEA KRVLRYYLFQ GQRYIWIETQ QAFYQVSLLD HGRSCDDVHR S RHGLSLQD QMVRKAIYGP NVISIPVKSY PQLLVDEALN PYYGFQAFSI ALWLADHYYW YALCIFLISS ISICLSLYKT RK QSQTLRD MVKLSMRVCV CRPGGEEEWV DSSELVPGDC LVLPQEGGLM PCDAALVAGE CMVNESSLTG ESIPVLKTAL PEG LGPYCA ETHRRHTLFC GTLILQARAY VGPHVLAVVT RTGFCTAKGG LVSSILHPRP INFKFYKHSM KFVAALSVLA LLGT IYSIF ILYRNRVPLN EIVIRALDLV TVVVPPALPA AMTVCTLYAQ SRLRRQGIFC IHPLRINLGG KLQLVCFDKT GTLTE DGLD VMGVVPLKGQ AFLPLVPEPR RLPVGPLLRA LATCHALSRL QDTPVGDPMD LKMVESTGWV LEEEPAADSA FGTQVL AVM RPPLWEPQLQ AMEEPPVPVS VLHRFPFSSA LQRMSVVVAW PGATQPEAYV KGSPELVAGL CNPETVPTDF AQMLQSY TA AGYRVVALAS KPLPTVPSLE AAQQLTRDTV EGDLSLLGLL VMRNLLKPQT TPVIQALRRT RIRAVMVTGD NLQTAVTV A RGCGMVAPQE HLIIVHATHP ERGQPASLEF LPMESPTAVN GVKDPDQAAS YTVEPDPRSR HLALSGPTFG IIVKHFPKL LPKVLVQGTV FARMAPEQKT ELVCELQKLQ YCVGMCGDGA NDCGALKAAD VGISLSQAEA SVVSPFTSSM ASIECVPMVI REGRCSLDT SFSVFKYMAL YSLTQFISVL ILYTINTNLG DLQFLAIDLV ITTTVAVLMS RTGPALVLGR VRPPGALLSV P VLSSLLLQ MVLVTGVQLG GYFLTLAQPW FVPLNRTVAA PDNLPNYENT VVFSLSSFQY LILAAAVSKG APFRRPLYTN VP FLVALAL LSSVLVGLVL VPGLLQGPLA LRNITDTGFK LLLLGLVTLN FVGAFMLESV LDQCLPACLR RLRPKRASKK RFK QLEREL AEQR

UniProtKB: Polyamine-transporting ATPase 13A2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242367
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more