+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36785 | |||||||||
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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: 3.33 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_36785.map.gz | 15.9 MB | EMDB map data format | |
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Header (meta data) | emd-36785-v30.xml emd-36785.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_36785.png | 38.2 KB | ||
Filedesc metadata | emd-36785.cif.gz | 5.7 KB | ||
Others | emd_36785_half_map_1.map.gz emd_36785_half_map_2.map.gz | 15.5 MB 15.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36785 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36785 | HTTPS FTP |
-Validation report
Summary document | emd_36785_validation.pdf.gz | 802.6 KB | Display | EMDB validaton report |
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Full document | emd_36785_full_validation.pdf.gz | 802.2 KB | Display | |
Data in XML | emd_36785_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | emd_36785_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36785 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36785 | HTTPS FTP |
-Related structure data
Related structure data | 8k13MC 8k10C 8k11C 8k12C 8k1bC 8k1dC 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_36785.map.gz / Format: CCP4 / Size: 16.8 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: 1.35 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36785_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36785_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
Entire | Name: human SID1 transmembrane family member 1 (SIDT1) homodimer |
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Components |
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-Supramolecule #1: human SID1 transmembrane family member 1 (SIDT1) homodimer
Supramolecule | Name: human SID1 transmembrane family member 1 (SIDT1) homodimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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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: 91.771867 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKANLLVLLC ALAAADASPG HPAKSPRQPP APRRDPFDAA RGADFDHVYS GVVNLSTENI YSFNYTSQPD QVTAVRVYVN SSSENLNYP VLVVVRQQKE VLSWQVPLLF QGLYQRSYNY QEVSRTLCPS EATNETGPLQ QLIFVDVASM APLGAQYKLL V TKLKHFQL ...String: MKANLLVLLC ALAAADASPG HPAKSPRQPP APRRDPFDAA RGADFDHVYS GVVNLSTENI YSFNYTSQPD QVTAVRVYVN SSSENLNYP VLVVVRQQKE VLSWQVPLLF QGLYQRSYNY QEVSRTLCPS EATNETGPLQ QLIFVDVASM APLGAQYKLL V TKLKHFQL RTNVAFHFTA SPSQPQYFLY KFPKDVDSVI IKVVSEMAYP CSVVSVQNIM CPVYDLDHNV EFNGVYQSMT KK AAITLQK KDFPGEQFFV VFVIKPEDYA CGGSFFIQEK ENQTWNLQRK KNLEVTIVPS IKESVYVKSS LFSVFIFLSF YLG CLLVGF VHYLRFQRKS IDGSFGSNDG SGNMVASHPI AASTPEPDIE SDKNIIRTKM FLYLSDLSRK DRRIVSKKYK IYFW NIITI AVFYALPVIQ LVITYQTVVN VTGNQDICYY NFLCAHPLGV LSAFNNILSN LGHVLLGFLF LLIVLRRDIL HRRAL EAKD IFAVEYGIPK HFGLFYAMGI ALMMEGVLSA CYHVCPNYSN FQFDTSFMYM IAGLCMLKLY QTRHPDINAS AYSAYA SFA VVIMVTVLGV VFGKNDVWFW VIFSAIHVLA SLALSTQIYY MGRFKIDLGI FRRAAMVFYT DCIQQCSRPL YMDRMVL LV VGNLVNWSFA LFGLIYRPRD FASYMLGIFI CNLLLYLAFY IIMKLRSSEK VLPVPLFCIV ATAVMWAAAL YFFFQNLS S WEGTPAESRE KNRECILLDF FDDHDIWHFL SATALFFSFL VLLTLDDDLD VVRRDQIPVF DYKDHDGDYK DHDIDYKDD DDK UniProtKB: SID1 transmembrane family member 1 |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149089 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |