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- PDB-9jbr: P5A-ATPase ATP13A1 D533N mutant -

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Basic information

Entry
Database: PDB / ID: 9jbr
TitleP5A-ATPase ATP13A1 D533N mutant
ComponentsEndoplasmic reticulum transmembrane helix translocase
KeywordsMEMBRANE PROTEIN / ER membrane / Transmembrane helices / Translocation / Mutant
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, Y. / Liao, J.
Funding support1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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


Theoretical massNumber of molelcules
Total (without water)120,3031
Polymers120,3031
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: 120303.336 Da / Num. of mol.: 1 / Mutation: D533N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP13A1, ATP13A, KIAA1825, CGI-152 / 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
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 D533N mutant / Type: COMPLEX / Details: ATP13A1 D533N mutant purified in GDN buffer / Entity ID: all / Source: RECOMBINANT
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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 4633

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Processing

EM software
IDNameCategory
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180661 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0068076
ELECTRON MICROSCOPYf_angle_d0.70710958
ELECTRON MICROSCOPYf_dihedral_angle_d4.9781079
ELECTRON MICROSCOPYf_chiral_restr0.0481272
ELECTRON MICROSCOPYf_plane_restr0.0051389

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