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- EMDB-64135: Cryo-EM structure of the Pma1 with ordered N-terminal extension i... -

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Basic information

Entry
Database: EMDB / ID: EMD-64135
TitleCryo-EM structure of the Pma1 with ordered N-terminal extension in the activated state
Map data
Sample
  • Cell: Cryo-EM structure of the Pma1 with ordered N-terminal extension in the activated state
    • Protein or peptide: Plasma membrane ATPase 1
KeywordsPma1 / Activated State / Proton Transport
Function / homology
Function and homology information


P-type H+-exporting transporter / eisosome / proton export across plasma membrane / proteasome storage granule assembly / P-type proton-exporting transporter activity / positive regulation of TORC1 signaling / proton transmembrane transport / regulation of intracellular pH / transmembrane transport / membrane raft ...P-type H+-exporting transporter / eisosome / proton export across plasma membrane / proteasome storage granule assembly / P-type proton-exporting transporter activity / positive regulation of TORC1 signaling / proton transmembrane transport / regulation of intracellular pH / transmembrane transport / membrane raft / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
P-type ATPase, subfamily IIIA / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / 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, subfamily IIIA / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Plasma membrane ATPase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsYou ZL / Bai L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171212 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the Pma1 with ordered N-terminal extension in the activated state
Authors: You ZL / Bai L
History
DepositionApr 11, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64135.png

Downloads & links

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Map

FileDownload / File: emd_64135.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.275175 - 4.3288503
Average (Standard dev.)0.0012255439 (±0.04657557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64135_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64135_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the Pma1 with ordered N-terminal extension i...

EntireName: Cryo-EM structure of the Pma1 with ordered N-terminal extension in the activated state
Components
  • Cell: Cryo-EM structure of the Pma1 with ordered N-terminal extension in the activated state
    • Protein or peptide: Plasma membrane ATPase 1

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Supramolecule #1: Cryo-EM structure of the Pma1 with ordered N-terminal extension i...

SupramoleculeName: Cryo-EM structure of the Pma1 with ordered N-terminal extension in the activated state
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Plasma membrane ATPase 1

MacromoleculeName: Plasma membrane ATPase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: P-type H+-exporting transporter
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 99.714023 KDa
SequenceString: MTDTSSSSSS SSASSVSAHQ PTQEKPAKTY DDAASESSDD DDIDALIEEL QSNHGVDDED SDNDGPVAAG EARPVPEEYL QTDPSYGLT SDEVLKRRKK YGLNQMADEK ESLVVKFVMF FVGPIQFVME AAAILAAGLS DWVDFGVICG LLMLNAGVGF V QEFQAGSI ...String:
MTDTSSSSSS SSASSVSAHQ PTQEKPAKTY DDAASESSDD DDIDALIEEL QSNHGVDDED SDNDGPVAAG EARPVPEEYL QTDPSYGLT SDEVLKRRKK YGLNQMADEK ESLVVKFVMF FVGPIQFVME AAAILAAGLS DWVDFGVICG LLMLNAGVGF V QEFQAGSI VDELKKTLAN TAVVIRDGQL VEIPANEVVP GDILQLEDGT VIPTDGRIVT EDCFLQIDQS AITGESLAVD KH YGDQTFS SSTVKRGEGF MVVTATGDNT FVGRAAALVN KAAGGQGHFT EVLNGIGIIL LVLVIATLLL VWTACFYRTN GIV RILRYT LGITIIGVPV GLPAVVTTTM AVGAAYLAKK QAIVQKLSAI ESLAGVEILC SDKTGTLTKN KLSLHEPYTV EGVS PDDLM LTACLAASRK KKGLDAIDKA FLKSLKQYPK AKDALTKYKV LEFHPFDPVS KKVTAVVESP EGERIVCVKG APLFV LKTV EEDHPIPEDV HENYENKVAE LASRGFRALG VARKRGEGHW EILGVMPCMD PPRDDTAQTV SEARHLGLRV KMLTGD AVG IAKETCRQLG LGTNIYNAER LGLGGGGDMP GSELADFVEN ADGFAEVFPQ HKYRVVEILQ NRGYLVAMTG DGVNDAP SL KKADTGIAVE GATDAARSAA DIVFLAPGLS AIIDALKTSR QIFHRMYSYV VYRIALSLHL EIFLGLWIAI LDNSLDID L IVFIAIFADV ATLAIAYDNA PYSPKPVKWN LPRLWGMSII LGIVLAIGSW ITLTTMFLPK GGIIQNFGAM NGIMFLQIS LTENWLIFIT RAAGPFWSSI PSWQLAGAVF AVDIIATMFT LFGWWSENWT DIVTVVRVWI WSIGIFCVLG GFYYEMSTSE AFDRLMNGK PMKEKKSTRS VEDFMAAMQR VSTQHEKET

UniProtKB: Plasma membrane ATPase 1

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
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: DARK FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: OTHER / Number images used: 205746
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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