+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31003 | |||||||||
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Title | WT transporter state1 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | : Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zhang Y / Watanabe S / Tsutsumi A / Inaba K | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: EMBO J / Year: 2021 Title: Cryo-EM analysis provides new mechanistic insight into ATP binding to Ca -ATPase SERCA2b. Authors: Yuxia Zhang / Satoshi Watanabe / Akihisa Tsutsumi / Hiroshi Kadokura / Masahide Kikkawa / Kenji Inaba / Abstract: Sarco/endoplasmic reticulum Ca -ATPase (SERCA) 2b is a ubiquitous SERCA family member that conducts Ca uptake from the cytosol to the ER. Herein, we present a 3.3 Å resolution cryo-electron ...Sarco/endoplasmic reticulum Ca -ATPase (SERCA) 2b is a ubiquitous SERCA family member that conducts Ca uptake from the cytosol to the ER. Herein, we present a 3.3 Å resolution cryo-electron microscopy (cryo-EM) structure of human SERCA2b in the E1·2Ca state, revealing a new conformation for Ca -bound SERCA2b with a much closer arrangement of cytosolic domains than in the previously reported crystal structure of Ca -bound SERCA1a. Multiple conformations generated by 3D classification of cryo-EM maps reflect the intrinsically dynamic nature of the cytosolic domains in this state. Notably, ATP binding residues of SERCA2b in the E1·2Ca state are located at similar positions to those in the E1·2Ca -ATP state; hence, the cryo-EM structure likely represents a preformed state immediately prior to ATP binding. Consistently, a SERCA2b mutant with an interdomain disulfide bridge that locks the closed cytosolic domain arrangement displayed significant autophosphorylation activity in the presence of Ca . We propose a novel mechanism of ATP binding to SERCA2b. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31003.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-31003-v30.xml emd-31003.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31003_fsc.xml | 6.1 KB | Display | FSC data file |
Images | emd_31003.png | 43.5 KB | ||
Masks | emd_31003_msk_1.map | 18.1 MB | Mask map | |
Others | emd_31003_additional_1.map.gz emd_31003_half_map_1.map.gz emd_31003_half_map_2.map.gz | 13.7 MB 13.8 MB 13.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31003 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31003 | HTTPS FTP |
-Validation report
Summary document | emd_31003_validation.pdf.gz | 610.5 KB | Display | EMDB validaton report |
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Full document | emd_31003_full_validation.pdf.gz | 610.1 KB | Display | |
Data in XML | emd_31003_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | emd_31003_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31003 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31003 | HTTPS FTP |
-Related structure data
Related structure data | 7e7sMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31003.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_31003_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_31003_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31003_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31003_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SERCA2b with Ca
Entire | Name: SERCA2b with Ca |
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Components |
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-Supramolecule #1: SERCA2b with Ca
Supramolecule | Name: SERCA2b with Ca / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 110 kDa/nm |
-Macromolecule #1: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Macromolecule | Name: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 / 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: 114.869664 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL LVRILLLAAC ISFVLAWFEE GEETITAFV EPFVILLILV ANAIVGVWQE RNAENAIEAL KEYEPEMGKV YRQDRKSVQR IKAKDIVPGD IVEIAVGDKV P ADIRLTSI ...String: MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL LVRILLLAAC ISFVLAWFEE GEETITAFV EPFVILLILV ANAIVGVWQE RNAENAIEAL KEYEPEMGKV YRQDRKSVQR IKAKDIVPGD IVEIAVGDKV P ADIRLTSI KSTTLRVDQS ILTGESVSVI KHTDPVPDPR AVNQDKKNML FSGTNIAAGK AMGVVVATGV NTEIGKIRDE MV ATEQERT PLQQKLDEFG EQLSKVISLI CIAVWIINIG HFNDPVHGGS WIRGAIYYFK IAVALAVAAI PEGLPAVITT CLA LGTRRM AKKNAIVRSL PSVETLGCTS VICSDKTGTL TTNQMSVCRM FILDRVEGDT CSLNEFTITG STYAPIGEVH KDDK PVNCH QYDGLVELAT ICALCNDSAL DYNEAKGVYE KVGEATETAL TCLVEKMNVF DTELKGLSKI ERANACNSVI KQLMK KEFT LEFSRDRKSM SVYCTPNKPS RTSMSKMFVK GAPEGVIDRC THIRVGSTKV PMTSGVKQKI MSVIREWGSG SDTLRC LAL ATHDNPLRRE EMHLEDSANF IKYETNLTFV GCVGMLDPPR IEVASSVKLC RQAGIRVIMI TGDNKGTAVA ICRRIGI FG QDEDVTSKAF TGREFDELNP SAQRDACLNA RCFARVEPSH KSKIVEFLQS FDEITAMTGD GVNDAPALKK AEIGIAMG S GTAVAKTASE MVLADDNFST IVAAVEEGRA IYNNMKQFIR YLISSNVGEV VCIFLTAALG FPEALIPVQL LWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAI FESPYPMTMA LSVLVTIEMC NALNSLSENQ SLLRMPPWEN IWLVGSICLS MSLHFLILYV EPLPLIFQIT P LNVTQWLM VLKISLPVIL MDETLKFVAR NYLEPGKECV QPATKSCSFS ACTDGISWPF VLLIMPLVIW VYSTDTNFSD MF WS |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |