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- PDB-9jbm: P5A-ATPase ATP13A1 reconstructed in nanodiscs -

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Basic information

Entry
Database: PDB / ID: 9jbm
TitleP5A-ATPase ATP13A1 reconstructed in nanodiscs
Components
  • Endoplasmic reticulum transmembrane helix translocase
  • Putative endogenous substrate
KeywordsMEMBRANE PROTEIN / ER membrane / Transmembrane helices / Translocation
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 / P-type ATPase actuator domain / 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 ...: / : / P5A-ATPase, transmembrane helical hairpin / P-type ATPase, subfamily V / P-type ATPase actuator domain / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsLi, Y. / Liao, J.
Funding support1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum transmembrane helix translocase
B: Putative endogenous substrate


Theoretical massNumber of molelcules
Total (without water)130,9732
Polymers130,9732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Endoplasmic reticulum transmembrane helix translocase / Endoplasmic reticulum P5A-ATPase


Mass: 129082.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP13A1, ATP13A, KIAA1825, CGI-152 / Plasmid: pEGBacMam / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human)
References: UniProt: Q9HD20, Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate
#2: Protein/peptide Putative endogenous substrate


Mass: 1890.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ATP13A1 with putative substrate in nanodiscs / Type: COMPLEX
Details: ATP13A1 purified in BeF3- buffer be reconstructed into nanodiscs
Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 GnTI- / Plasmid: pEGBacMam
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMSodium chlorideNaCl1
35 mMMagnesium chlorideMgCl21
40.006 %Glyco-diosgeninGDN1
52 mMBeryllium sulfateBeSO41
610 mMSodium fluorideNaF1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4895

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Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
8PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: NONE
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82168 / Symmetry type: POINT
RefinementHighest resolution: 3.83 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058840
ELECTRON MICROSCOPYf_angle_d1.14312009
ELECTRON MICROSCOPYf_dihedral_angle_d5.5481186
ELECTRON MICROSCOPYf_chiral_restr0.0581408
ELECTRON MICROSCOPYf_plane_restr0.0111516

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