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- EMDB-42943: Structure of the human systemic RNAi defective transmembrane prot... -
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Open data
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Basic information
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Title | Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) | |||||||||
![]() | Sharpened map resulting from local refinement in cryosparc | |||||||||
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![]() | RNA interference / transmembrane protein / cholesterol or dsRNA uptake family. / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() NNS virus cap methyltransferase / RNA transmembrane transporter activity / GDP polyribonucleotidyltransferase / RNA transport / cholesterol binding / bioluminescence / generation of precursor metabolites and energy / double-stranded RNA binding / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm ...NNS virus cap methyltransferase / RNA transmembrane transporter activity / GDP polyribonucleotidyltransferase / RNA transport / cholesterol binding / bioluminescence / generation of precursor metabolites and energy / double-stranded RNA binding / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / lysosome / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Navratna V / Kumar A / Rana JK / Mosalaganti S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain Authors: Navratna V / Kumar A / Rana JK / Mosalaganti S | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 167.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.4 KB 22.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12 KB | Display | ![]() |
Images | ![]() | 91.2 KB | ||
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() ![]() ![]() | 88.2 MB 994 KB 164.9 MB 164.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 26.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v38MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharpened map resulting from local refinement in cryosparc | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: UnSharpened map resulting from local refinement in cryosparc
File | emd_42943_additional_1.map | ||||||||||||
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Annotation | UnSharpened map resulting from local refinement in cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Mask Used for refinement during local refinement refinement...
File | emd_42943_additional_2.map | ||||||||||||
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Annotation | Mask Used for refinement during local refinement refinement of symmetry expanded particles in cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map resulting from Local refinement in cryosparc
File | emd_42943_half_map_1.map | ||||||||||||
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Annotation | Half map resulting from Local refinement in cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map resulting from Local refinement in cryosparc
File | emd_42943_half_map_2.map | ||||||||||||
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Annotation | Half map resulting from Local refinement in cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human systemic RNAi defective transmembrane protein 1 (hSIDT1)
Entire | Name: Human systemic RNAi defective transmembrane protein 1 (hSIDT1) |
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Components |
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-Supramolecule #1: Human systemic RNAi defective transmembrane protein 1 (hSIDT1)
Supramolecule | Name: Human systemic RNAi defective transmembrane protein 1 (hSIDT1) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Full length human SIDT1 expressed as a recombinant fusion protein with N-terminal GFP, in mammalian cells |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 123.9 KDa |
-Macromolecule #1: SID1 transmembrane family member 1,RNA-directed RNA polymerase L
Macromolecule | Name: SID1 transmembrane family member 1,RNA-directed RNA polymerase L type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: NNS virus cap methyltransferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 124.098141 KDa |
Recombinant expression | Organism: ![]() |
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 EGVLSA 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 RDQIPVFAAA FESRLEVLFQ GPAAAAVSKG EELFTGVVPI LVELDGDVNG HKFSVSGEGE GDATYGKLT LKFICTTGKL PVPWPTLVTT LTYGVQCFSR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRAEVK F EGDTLVNR IELKGIDFKE DGNILGHKLE YNYNSHNVYI MADKQKNGIK VNFKIRHNIE DGSVQLADHY QQNTPIGDGP VL LPDNHYL STQSKLSKDP NEKRDHMVLL EFVTAAGITL GMDELYKSGG SGWSHPQFEK UniProtKB: SID1 transmembrane family member 1, RNA-directed RNA polymerase L |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.026000000000000002 kPa / Details: 15 mA current | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | hSIDT1 in digitonin micelle, purified by Strep-Tactin affinity chromatography |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 17000 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: in silico model / Details: Made using Model angelo |
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Refinement | Protocol: RIGID BODY FIT |
Output model | ![]() PDB-8v38: |