+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36792 | |||||||||
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Title | SID1 transmembrane family member 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / TRANSPORT PROTEIN | |||||||||
Function / homology | RNA transmembrane transporter activity / SID1 transmembrane family / dsRNA-gated channel SID-1 / RNA transport / cholesterol binding / double-stranded RNA binding / lysosome / plasma membrane / SID1 transmembrane family member 1 Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.53 Å | |||||||||
Authors | Guo H / Qi C / Lu Y / Yang H / Zhu Y / Sun F / Ji X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity. Authors: Le Zheng / Tingting Yang / Hangtian Guo / Chen Qi / Yuchi Lu / Haonan Xiao / Yan Gao / Yue Liu / Yixuan Yang / Mengru Zhou / Henry C Nguyen / Yun Zhu / Fei Sun / Chen-Yu Zhang / Xiaoyun Ji / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36792.map.gz | 15.9 MB | EMDB map data format | |
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Header (meta data) | emd-36792-v30.xml emd-36792.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_36792.png | 30.6 KB | ||
Filedesc metadata | emd-36792.cif.gz | 5.5 KB | ||
Others | emd_36792_half_map_1.map.gz emd_36792_half_map_2.map.gz | 15.5 MB 15.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36792 | HTTPS FTP |
-Validation report
Summary document | emd_36792_validation.pdf.gz | 848.5 KB | Display | EMDB validaton report |
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Full document | emd_36792_full_validation.pdf.gz | 848.1 KB | Display | |
Data in XML | emd_36792_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | emd_36792_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36792 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36792 | HTTPS FTP |
-Related structure data
Related structure data | 8k1dMC 8k10C 8k11C 8k12C 8k13C 8k1bC 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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-Map
File | Download / File: emd_36792.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36792_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36792_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD f...
Entire | Name: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD focused refinement |
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Components |
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-Supramolecule #1: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD f...
Supramolecule | Name: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD focused refinement type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SID1 transmembrane family member 1
Macromolecule | Name: SID1 transmembrane family member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 58.291754 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: IKESVYVKSS LFSVFIFLSF YLGCLLVGFV HYLRFQRKSI DGSFGSNDGS GNMVASHPIA ASTPEPDIES DKNIIRTKMF LYLSDLSRK DRRIVSKKYK IYFWNIITIA VFYALPVIQL VITYQTVVNV TGNQDICYYN FLCAHPLGVL SAFNNILSNL G HVLLGFLF ...String: IKESVYVKSS LFSVFIFLSF YLGCLLVGFV HYLRFQRKSI DGSFGSNDGS GNMVASHPIA ASTPEPDIES DKNIIRTKMF LYLSDLSRK DRRIVSKKYK IYFWNIITIA VFYALPVIQL VITYQTVVNV TGNQDICYYN FLCAHPLGVL SAFNNILSNL G HVLLGFLF LLIVLRRDIL HRRALEAKDI FAVEYGIPKH FGLFYAMGIA LMMEGVLSAC YHVCPNYSNF QFDTSFMYMI AG LCMLKLY QTRHPDINAS AYSAYASFAV VIMVTVLGVV FGKNDVWFWV IFSAIHVLAS LALSTQIYYM GRFKIDLGIF RRA AMVFYT DCIQQCSRPL YMDRMVLLVV GNLVNWSFAL FGLIYRPRDF ASYMLGIFIC NLLLYLAFYI IMKLRSSEKV LPVP LFCIV ATAVMWAAAL YFFFQNLSSW EGTPAESREK NRECILLDFF DDHDIWHFLS ATALFFSFLV LLTLDDDLDV VRRDQ IPVF DYKDHDGDYK DHDIDYKDDD DK UniProtKB: SID1 transmembrane family member 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K3 (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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81463 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |