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- EMDB-13011: Cryo-EM structure of P5B-ATPase E2PiAlF/SPM -

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Basic information

Entry
Database: EMDB / ID: EMD-13011
TitleCryo-EM structure of P5B-ATPase E2PiAlF/SPM
Map data
Sample
  • Cell: P5B-ATPase
    • Protein or peptide: Cation-transporting ATPase
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: SPERMINE
KeywordsSPM transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / P-type ion transporter activity / ATPase-coupled monoatomic cation transmembrane transporter activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
Similarity search - Function
Hypothetical cof family signature 2. / : / : / P5-type ATPase cation transporter / P-type ATPase, subfamily V / 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 ...Hypothetical cof family signature 2. / : / : / P5-type ATPase cation transporter / P-type ATPase, subfamily V / 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 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Cation-transporting ATPase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi P / Gourdon P
Funding support Sweden, Denmark, 4 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2020.0194, 2015.0131 Sweden
LundbeckfondenR313-2019-774, R218-2016-1548, R133-A12689 Denmark
Danish Council for Independent Research9039-00273, 6108-00479 Denmark
Swedish Research Council2016-04474 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: Structure and transport mechanism of P5B-ATPases.
Authors: Ping Li / Kaituo Wang / Nina Salustros / Christina Grønberg / Pontus Gourdon /
Abstract: In human cells, P5B-ATPases execute the active export of physiologically important polyamines such as spermine from lysosomes to the cytosol, a function linked to a palette of disorders. Yet, the ...In human cells, P5B-ATPases execute the active export of physiologically important polyamines such as spermine from lysosomes to the cytosol, a function linked to a palette of disorders. Yet, the overall shape of P5B-ATPases and the mechanisms of polyamine recognition, uptake and transport remain elusive. Here we describe a series of cryo-electron microscopy structures of a yeast homolog of human ATP13A2-5, Ypk9, determined at resolutions reaching 3.4 Å, and depicting three separate transport cycle intermediates, including spermine-bound conformations. Surprisingly, in the absence of cargo, Ypk9 rests in a phosphorylated conformation auto-inhibited by the N-terminus. Spermine uptake is accomplished through an electronegative cleft lined by transmembrane segments 2, 4 and 6. Despite the dramatically different nature of the transported cargo, these findings pinpoint shared principles of transport and regulation among the evolutionary related P4-, P5A- and P5B-ATPases. The data also provide a framework for analysis of associated maladies, such as Parkinson's disease.
History
DepositionMay 28, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7op1
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13011.png

Downloads & links

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Map

FileDownload / File: emd_13011.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.744 Å		0.86 Å/pix.
x 320 pix.
= 275.744 Å		0.86 Å/pix.
x 320 pix.
= 275.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.35
Minimum - Maximum-1.4034266 - 2.3869212
Average (Standard dev.)0.0007917624 (±0.053869557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.744 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.86170.86170.8617
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z275.744275.744275.744
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.4032.3870.001

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Supplemental data

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Sample components

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Entire : P5B-ATPase

EntireName: P5B-ATPase
Components
  • Cell: P5B-ATPase
    • Protein or peptide: Cation-transporting ATPase
  • Ligand: MAGNESIUM ION
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: SPERMINE

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Supramolecule #1: P5B-ATPase

SupramoleculeName: P5B-ATPase / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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Macromolecule #1: Cation-transporting ATPase

MacromoleculeName: Cation-transporting ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 156.013906 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDGSRGTAPG GDDLRGDRRD SYQGEDREDS HLLGALEDGN HQQSQGHGGG SGFYHHNVNS SSASVLEGVE MAHDELFAGP VAESVPTSV SAFSHRHGRA ESVASFSFYH EQDDQREELE APPGSLGARL SIDDLDELPF EEEGLSESEM PEQLDTFGID L EWGSMNNG ...String:
MDGSRGTAPG GDDLRGDRRD SYQGEDREDS HLLGALEDGN HQQSQGHGGG SGFYHHNVNS SSASVLEGVE MAHDELFAGP VAESVPTSV SAFSHRHGRA ESVASFSFYH EQDDQREELE APPGSLGARL SIDDLDELPF EEEGLSESEM PEQLDTFGID L EWGSMNNG YPLIRRSSTH SQFSAHHRLL RRESGVSAAS GYTGGRSSQK MRLDNDDLTI AISGFITNRI GFAIYIVLCV LT GGIAWLF LRWYPKYYVK LVGCATPFRD CQWVVIEDHF NKMTILSIRV KPYNRPLSTV FGTPSRATSW PLAQDPDPVL REL RSITYC YYKFYYHPVL DKFFCCNGWK DPQWNSMQNA RSGLHGDEKA HREAVFGPNS IDVDEQSILQ LLVSEILTPF YAFQ VFSLI LWLCDEYYYY AAAILLISAG SIITSLLETK ETRRRLREMS RFECEVRVFR GGFWRTFPSS DLVPGDVYEV SDPSL TQIP ADSLLLTGDC IVNESMLTGE SVAVSKTPAT NETLAKLNPA ASTFSHDVDK HFLYCGTKLI RARQRLADTD EAAAVA LVV RTGFNTTRGA LVRSMLVPKP SKFKFYEDSF RYLKVMGCLA GLAFIVSLVN FIRLKLHWTL ILLRALDLLT IVVPPAL PA TLTIGTSFAV QRLKGKKIFC TSPQRVNVGG KIDLMCFDKT GTLTEEGLDV LGIRVASRVS NRFTELLTNV DDLTWSCD S VSNGDEVKPA DHVDGSSLKK DKTKPLDPYR AALYVMASCH SLRIVDGVAV GDPLEVKMFE FTGWSYEEGF IAGEVISTE GRGDISPSIA RPPRYMTSQE MSIGEAPPAV GVLRAFDFNP LLRRSSVIAR VVGNSGGYAL VKGSPECMPE ICRPETLPSD FDELLSYYT HAGYRVIACA TKRIPKLNLV SVNRMTRDEV ESGLDFVGFI IFENKLKPTT TSVIKELLSS NIGTVMITGD N IRTAVSVA RQCGIIEEHA HCYMPRFIEG NADDCNAKLR WESINNPALE LDPWTLLPMP VPPQTDASLP YDVSNIRNYA IA VTGDVFR WIVDHAPTDV LHRMLVLGKV YARMSPDEKQ ELVKKFQSID YSCGFCGDGA NDCAALKAAD VGISLSEAEA SVA APFTSQ IFDIRCVPEV IREGRASLVT SFSCFKYMSL YSFIQFTSVS FLYVSASNLG DFQFLYIDLM LILPIAVFMS WAGP HSKLC AKRPVSDLVS RKVLVPLLSH VFVCVMIQAL AWVAVRQQPW YIPPIVDTEK SNIENSENTT LFFASCFEYI LSGVV LNAG RPFRQSPLET WPFLSAVAVT LIATLLMLLV PPYWLFEFMQ LTWMSWTFKI TLIAFGFVYF LIAWTGEHYL FLWLAR FLG RMRQRLFKQP KQRKLYKIVK EKLVFENLYF

UniProtKB: Cation-transporting ATPase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Macromolecule #4: SPERMINE

MacromoleculeName: SPERMINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SPM
Molecular weightTheoretical: 202.34 Da
Chemical component information

ChemComp-SPM:
SPERMINE

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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
VitrificationCryogen name: ETHANE

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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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7op3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 59345
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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