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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13013 | |||||||||||||||
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Title | Cryo-EM structure of P5B-ATPase E2P | |||||||||||||||
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![]() | SPM transporter / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | ![]() Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / polyamine transmembrane transporter activity / P-type ion transporter activity / ATPase-coupled monoatomic cation transmembrane transporter activity / intracellular calcium ion homeostasis / late endosome membrane / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
![]() | Li P / Gourdon P | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 417.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.2 KB 11.2 KB | Display Display | ![]() |
Images | ![]() | 39.5 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7op5MC ![]() 7op1C ![]() 7op3C ![]() 7op8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.54295 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : P5B-ATPase
Entire | Name: P5B-ATPase |
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Components |
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-Supramolecule #1: P5B-ATPase
Supramolecule | Name: P5B-ATPase / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: P5B-ATPase
Macromolecule | Name: P5B-ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 155.347188 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 EKLVF UniProtKB: Cation-transporting ATPase |
-Macromolecule #2: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ![]() ChemComp-BEF: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141028 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |