+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33717 | |||||||||
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Title | CryoEM structure of SPCA1a in E2P state | |||||||||
Map data | primary map for SPCA1a in E2P state | |||||||||
Sample |
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Function / homology | Function and homology information Golgi calcium ion homeostasis / Golgi calcium ion transport / P-type manganese transporter activity / trans-Golgi network membrane organization / manganese ion transport / intracellular manganese ion homeostasis / cis-Golgi network membrane / P-type Ca2+ transporter / P-type calcium transporter activity / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...Golgi calcium ion homeostasis / Golgi calcium ion transport / P-type manganese transporter activity / trans-Golgi network membrane organization / manganese ion transport / intracellular manganese ion homeostasis / cis-Golgi network membrane / P-type Ca2+ transporter / P-type calcium transporter activity / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of Golgi to plasma membrane protein transport / Golgi cisterna membrane / Ion transport by P-type ATPases / epidermis development / calcium ion transmembrane transport / trans-Golgi network / intracellular calcium ion homeostasis / calcium ion transport / manganese ion binding / actin cytoskeleton organization / positive regulation of canonical NF-kappaB signal transduction / Golgi membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Chen Z / Watanabe S / Inaba K | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Cryo-EM structures of human SPCA1a reveal the mechanism of Ca/Mn transport into the Golgi apparatus. Authors: Zhenghao Chen / Satoshi Watanabe / Hironori Hashida / Michio Inoue / Yasukazu Daigaku / Masahide Kikkawa / Kenji Inaba / Abstract: Secretory pathway Ca/Mn ATPase 1 (SPCA1) actively transports cytosolic Ca and Mn into the Golgi lumen, playing a crucial role in cellular calcium and manganese homeostasis. Detrimental mutations of ...Secretory pathway Ca/Mn ATPase 1 (SPCA1) actively transports cytosolic Ca and Mn into the Golgi lumen, playing a crucial role in cellular calcium and manganese homeostasis. Detrimental mutations of the gene encoding SPCA1 cause Hailey-Hailey disease. Here, using nanobody/megabody technologies, we determined cryo-electron microscopy structures of human SPCA1a in the ATP and Ca/Mn-bound (E1-ATP) state and the metal-free phosphorylated (E2P) state at 3.1- to 3.3-Å resolutions. The structures revealed that Ca and Mn share the same metal ion-binding pocket with similar but notably different coordination geometries in the transmembrane domain, corresponding to the second Ca-binding site in sarco/endoplasmic reticulum Ca-ATPase (SERCA). In the E1-ATP to E2P transition, SPCA1a undergoes similar domain rearrangements to those of SERCA. Meanwhile, SPCA1a shows larger conformational and positional flexibility of the second and sixth transmembrane helices, possibly explaining its wider metal ion specificity. These structural findings illuminate the unique mechanisms of SPCA1a-mediated Ca/Mn transport. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33717.map.gz | 2.2 MB | EMDB map data format | |
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Header (meta data) | emd-33717-v30.xml emd-33717.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_33717.png | 121.5 KB | ||
Masks | emd_33717_msk_1.map | 64 MB | Mask map | |
Others | emd_33717_half_map_1.map.gz emd_33717_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33717 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33717 | HTTPS FTP |
-Related structure data
Related structure data | 7yamMC 7yagC 7yahC 7yaiC 7yajC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33717.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | primary map for SPCA1a in E2P state | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.16719 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33717_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33717_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33717_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPCA1a in E2P state
Entire | Name: SPCA1a in E2P state |
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Components |
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-Supramolecule #1: SPCA1a in E2P state
Supramolecule | Name: SPCA1a in E2P state / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Calcium-transporting ATPase type 2C member 1
Macromolecule | Name: Calcium-transporting ATPase type 2C member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Ca2+ transporter |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 103.574203 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGGVAMPGAE DDVVRENLYF QGKDGLAAMK VARFQKIPNG ENETMIPVLT SKKASELPVS EVASILQADL QNGLNKCEVS HRRAFHGWN EFDISEDEPL WKKYISQFKN PLIMLLLASA VISVLMHQFD DAVSITVAIL IVVTVAFVQE YRSEKSLEEL S KLVPPECH ...String: MGGVAMPGAE DDVVRENLYF QGKDGLAAMK VARFQKIPNG ENETMIPVLT SKKASELPVS EVASILQADL QNGLNKCEVS HRRAFHGWN EFDISEDEPL WKKYISQFKN PLIMLLLASA VISVLMHQFD DAVSITVAIL IVVTVAFVQE YRSEKSLEEL S KLVPPECH CVREGKLEHT LARDLVPGDT VCLSVGDRVP ADLRLFEAVD LSIDESSLTG ETTPCSKVTA PQPAATNGDL AS RSNIAFM GTLVRCGKAK GVVIGTGENS EFGEVFKMMQ AEEAPKTPLQ KSMDLLGKQL SFYSFGIIGI IMLVGWLLGK DIL EMFTIS VSLAVAAIPE GLPIVVTVTL ALGVMRMVKK RAIVKKLPIV ETLGCCNVIC SDKTGTLTKN EMTVTHIFTS DGLH AEVTG VGYNQFGEVI VDGDVVHGFY NPAVSRIVEA GCVCNDAVIR NNTLMGKPTE GALIALAMKM GLDGLQQDYI RKAEY PFSS EQKWMAVKCV HRTQQDRPEI CFMKGAYEQV IKYCTTYQSK GQTLTLTQQQ RDVYQQEKAR MGSAGLRVLA LASGPE LGQ LTFLGLVGII DPPRTGVKEA VTTLIASGVS IKMITGDSQE TAVAIASRLG LYSKTSQSVS GEEIDAMDVQ QLSQIVP KV AVFYRASPRH KMKIIKSLQK NGSVVAMTGD GVNDAVALKA ADIGVAMGQT GTDVCKEAAD MILVDDDFQT IMSAIEEG K GIYNNIKNFV RFQLSTSIAA LTLISLATLM NFPNPLNAMQ ILWINIIMDG PPAQSLGVEP VDKDVIRKPP RNWKDSILT KNLILKILVS SIIIVCGTLF VFWRELRDNV ITPRDTTMTF TCFVFFDMFN ALSSRSQTKS VFEIGLCSNR MFCYAVLGSI MGQLLVIYF PPLQKVFQTE SLSILDLLFL LGLTSSVCIV AEIIKKVERS REKIQKHVSS TSSSFLEV |
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260172 |