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- EMDB-61319: P5A-ATPase ATP13A1 reconstructed in nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-61319
TitleP5A-ATPase ATP13A1 reconstructed in nanodiscs
Map dataConsensus map
Sample
  • Complex: ATP13A1 with putative substrate in nanodiscs
    • Protein or peptide: Endoplasmic reticulum transmembrane helix translocase
    • Protein or peptide: Putative endogenous substrate
KeywordsER membrane / Transmembrane helices / Translocation / 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: 3.83 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_61319.png

Downloads & links

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Map

FileDownload / File: emd_61319.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: 0.052
Minimum - Maximum-0.001712725 - 1.8739237
Average (Standard dev.)0.0033212402 (±0.04152609)
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_61319_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_61319_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_61319_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 with putative substrate in nanodiscs

EntireName: ATP13A1 with putative substrate in nanodiscs
Components
  • Complex: ATP13A1 with putative substrate in nanodiscs
    • Protein or peptide: Endoplasmic reticulum transmembrane helix translocase
    • Protein or peptide: Putative endogenous substrate

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Supramolecule #1: ATP13A1 with putative substrate in nanodiscs

SupramoleculeName: ATP13A1 with putative substrate in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: ATP13A1 purified in BeF3- buffer be reconstructed into nanodiscs
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: 129.082664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LAAGPALIAN GDELVAAVWP YRRLALLRRL TVLPFAGLLY PAWLGAAAAG CWGWGSSWVQ IPEAALLVLA TICLAHALTV LSGHWSVHA HCALTCTPEY DPSKATFVKV VPTPNNGSTE LVALHRNEGE DGLEVLSFEF QKIKYSYDAL EKKQFLPVAF P VGNAFSYY ...String:
LAAGPALIAN GDELVAAVWP YRRLALLRRL TVLPFAGLLY PAWLGAAAAG CWGWGSSWVQ IPEAALLVLA TICLAHALTV LSGHWSVHA HCALTCTPEY DPSKATFVKV VPTPNNGSTE LVALHRNEGE DGLEVLSFEF QKIKYSYDAL EKKQFLPVAF P VGNAFSYY QSNRGFQEDS EIRAAEKKFG SNKAEMVVPD FSELFKERAT APFFVFQVFC VGLWCLDEYW YYSVFTLSML VA FEASLVQ QQMRNMSEIR KMGNKPHMIQ VYRSRKWRPI ASDEIVPGDI VSIGRSPQEN LVPCDVLLLR GRCIVDEAML TGE SVPQMK EPIEDLSPDR VLDLQADSRL HVIFGGTKVV QHIPPQKATT GLKPVDSGCV AYVLRTGFNT SQGKLLRTIL FGVK RVTAN NLETFIFILF LLVFAIAAAA YVWIEGTKDP SRNRYKLFLE CTLILTSVVP PELPIELSLA VNTSLIALAK LYMYC TEPF RIPFAGKVEV CCFDKTGTLT SDSLVVRGVA GLRDGKEVTP VSSIPVETHR ALASCHSLMQ LDDGTLVGDP LEKAML TAV DWTLTKDEKV FPRSIKTQGL KIHQRFHFAS ALKRMSVLAS YEKLGSTDLC YIAAVKGAPE TLHSMFSQCP PDYHHIH TE ISREGARVLA LGYKELGHLT HQQAREVKRE ALECSLKFVG FIVVSCPLKA DSKAVIREIQ NASHRVVMIT GDNPLTAC H VAQELHFIEK AHTLILQPPS EKGRQCEWRS IDGSIVLPLA RGSPKALALE YALCLTGDGL AHLQATDPQQ LLRLIPHVQ VFARVAPKQK EFVITSLKEL GYVTLMCGDG TNDVGALKHA DVGVALLANA PERVVERRRR PRDSPTLSNS GIRATSRTAK QRSGLPPSE EQPTSQRDRL SQVLRDLEDE STPIVKLGDA SIAAPFTSKL SSIQCICHVI KQGRCTLVTT LQMFKILALN A LILAYSQS VLYLEGVKFS DFQATLQGLL LAGCFLFISR SKPLKTLSRE RPLPNIFNLY TILTVMLQFF VHFLSLVYLY RE AQARSPE KQEQFVDLYK EFEPSLVNST VYIMAMAMQM ATFAINYKGP PFMESLPENK PLVWSLAVSL LAIIGLLLGS SPD FNSQFG LVDIPVEFKL VIAQVLLLDF CLALLADRVL QFFLGTP

UniProtKB: Endoplasmic reticulum transmembrane helix translocase

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Macromolecule #2: Putative endogenous substrate

MacromoleculeName: Putative endogenous substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.890321 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
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: 4895 / 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: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82168
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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