+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36662 | |||||||||
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Title | Cryo-EM structure of SIDT1 E555Q mutant | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SID-1 transmembrane family member 1 / CREST family / phospholipase D / RNA uptake / MEMBRANE 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: 2.38 Å | |||||||||
Authors | Sun CR / Xu D / Li Q / Zhou CZ / Chen Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Human SIDT1 mediates dsRNA uptake via its phospholipase activity. Authors: Cai-Rong Sun / Da Xu / Fengrui Yang / Zhuanghao Hou / Yuyao Luo / Chen-Yu Zhang / Ge Shan / Guangming Huang / Xuebiao Yao / Yuxing Chen / Qiong Li / Cong-Zhao Zhou / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36662.map.gz | 49.7 MB | EMDB map data format | |
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Header (meta data) | emd-36662-v30.xml emd-36662.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_36662.png | 123.6 KB | ||
Filedesc metadata | emd-36662.cif.gz | 5.7 KB | ||
Others | emd_36662_half_map_1.map.gz emd_36662_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36662 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36662 | HTTPS FTP |
-Validation report
Summary document | emd_36662_validation.pdf.gz | 841.3 KB | Display | EMDB validaton report |
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Full document | emd_36662_full_validation.pdf.gz | 840.9 KB | Display | |
Data in XML | emd_36662_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_36662_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36662 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36662 | HTTPS FTP |
-Related structure data
Related structure data | 8junMC 8julC 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_36662.map.gz / Format: CCP4 / Size: 52.7 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: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36662_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36662_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of SIDT1 E555Q mutant
Entire | Name: Cryo-EM structure of SIDT1 E555Q mutant |
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Components |
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-Supramolecule #1: Cryo-EM structure of SIDT1 E555Q mutant
Supramolecule | Name: Cryo-EM structure of SIDT1 E555Q mutant / 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: 93.922266 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MRGCLRLALL CALPWLLLAA SPGHPAKSPR QPPAPRRDPF DAARGADFDH VYSGVVNLST ENIYSFNYTS QPDQVTAVRV YVNSSSENL NYPVLVVVRQ QKEVLSWQVP LLFQGLYQRS YNYQEVSRTL CPSEATNETG PLQQLIFVDV ASMAPLGAQY K LLVTKLKH ...String: MRGCLRLALL CALPWLLLAA SPGHPAKSPR QPPAPRRDPF DAARGADFDH VYSGVVNLST ENIYSFNYTS QPDQVTAVRV YVNSSSENL NYPVLVVVRQ QKEVLSWQVP LLFQGLYQRS YNYQEVSRTL CPSEATNETG PLQQLIFVDV ASMAPLGAQY K LLVTKLKH FQLRTNVAFH FTASPSQPQY FLYKFPKDVD SVIIKVVSEM AYPCSVVSVQ NIMCPVYDLD HNVEFNGVYQ SM TKKAAIT LQKKDFPGEQ FFVVFVIKPE DYACGGSFFI QEKENQTWNL QRKKNLEVTI VPSIKESVYV KSSLFSVFIF LSF YLGCLL VGFVHYLRFQ RKSIDGSFGS NDGSGNMVAS HPIAASTPEG SNYGTIDESS SSPGRQMSSS DGGPPGQSDT DSSV EESDF DTMPDIESDK NIIRTKMFLY LSDLSRKDRR IVSKKYKIYF WNIITIAVFY ALPVIQLVIT YQTVVNVTGN QDICY YNFL CAHPLGVLSA FNNILSNLGH VLLGFLFLLI VLRRDILHRR ALEAKDIFAV EYGIPKHFGL FYAMGIALMM QGVLSA CYH VCPNYSNFQF DTSFMYMIAG LCMLKLYQTR HPDINASAYS AYASFAVVIM VTVLGVVFGK NDVWFWVIFS AIHVLAS LA LSTQIYYMGR FKIDLGIFRR AAMVFYTDCI QQCSRPLYMD RMVLLVVGNL VNWSFALFGL IYRPRDFASY MLGIFICN L LLYLAFYIIM KLRSSEKVLP VPLFCIVATA VMWAAALYFF FQNLSSWEGT PAESREKNRE CILLDFFDDH DIWHFLSAT ALFFSFLVLL TLDDDLDVVR RDQIPVF UniProtKB: SID1 transmembrane family member 1 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 3 / Number of copies: 2 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-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: 278 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1098736 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |