+Open data
-Basic information
Entry | Database: PDB / ID: 7e7s | ||||||
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Title | WT transporter state1 | ||||||
Components | Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 | ||||||
Keywords | METAL TRANSPORT / calcium | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Zhang, Y. / Watanabe, S. / Tsutsumi, A. / Inaba, K. | ||||||
Funding support | Japan, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7e7s.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e7s.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 7e7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e7s_validation.pdf.gz | 920.7 KB | Display | wwPDB validaton report |
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Full document | 7e7s_full_validation.pdf.gz | 929.7 KB | Display | |
Data in XML | 7e7s_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 7e7s_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/7e7s ftp://data.pdbj.org/pub/pdb/validation_reports/e7/7e7s | HTTPS FTP |
-Related structure data
Related structure data | 31003MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 114869.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATP2A2, ATP2B / Production host: Homo sapiens (human) / References: UniProt: P16615, P-type Ca2+ transporter | ||
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#2: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SERCA2b with Ca / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 110 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96416 / Symmetry type: POINT | ||||||||||||||||||||||||
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