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- PDB-8wor: Cryo-EM structure of human SIDT1 protein with C2 symmetry at neut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wor | ||||||
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Title | Cryo-EM structure of human SIDT1 protein with C2 symmetry at neutral pH | ||||||
![]() | SID1 transmembrane family member 1 | ||||||
![]() | HYDROLASE / Ceramidase / putative RNA and cholesterol transport protein | ||||||
Function / homology | ![]() RNA transmembrane transporter activity / RNA transport / cholesterol binding / double-stranded RNA binding / lysosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å | ||||||
![]() | Liu, W. / Tang, M. / Wang, J. / Zhang, X. / Wu, S. / Ru, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into cholesterol transport and hydrolase activity of a putative human RNA transport protein SIDT1. Authors: Wenxia Liu / Mengyuan Tang / Jiening Wang / Fangfang Wang / Gaojie Song / Xiaokang Zhang / Shan Wu / Heng Ru / ![]() | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.8 KB | Display | ![]() |
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PDB format | ![]() | 234.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 61.5 KB | Display | |
Data in CIF | ![]() | 88.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37696MC ![]() 8woqC ![]() 8wosC ![]() 8wotC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 99695.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 2 types, 8 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 27 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/SPL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/SPL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #6: Chemical | ChemComp-CLR / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Ternary complex of SIDT1 in complex with unknown lipids Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 52.52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 503286 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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