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Yorodumi- PDB-8v38: Structure of the human systemic RNAi defective transmembrane prot... -
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-Basic information
Entry | Database: PDB / ID: 8v38 | ||||||
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Title | Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) | ||||||
Components | SID1 transmembrane family member 1,RNA-directed RNA polymerase L | ||||||
Keywords | MEMBRANE PROTEIN / RNA interference / transmembrane protein / cholesterol or dsRNA uptake family. | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Navratna, V. / Kumar, A. / Rana, J.K. / Mosalaganti, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: bioRxiv / Year: 2024 Title: Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. Authors: Vikas Navratna / Arvind Kumar / Jaimin K Rana / Shyamal Mosalaganti / Abstract: In , inter-cellular transport of the small non-coding RNA causing systemic RNA interference (RNAi) is mediated by the transmembrane protein SID1, encoded by the gene in the systemic RNA interference- ...In , inter-cellular transport of the small non-coding RNA causing systemic RNA interference (RNAi) is mediated by the transmembrane protein SID1, encoded by the gene in the systemic RNA interference-defective () loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the cholesterol uptake family (ChUP). Although systemic RNAi is not an evolutionarily conserved process, the gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of gene products - hSIDT1 and hSIDT2 - mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain (ECD) of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain (TMD) exists as two modules - a flexible lipid binding domain (LBD) and a rigid TMD core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in cholesterol uptake (ChUP) family members. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v38.cif.gz | 313.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v38.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 8v38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v38_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8v38_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8v38_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 8v38_validation.cif.gz | 73.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/8v38 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/8v38 | HTTPS FTP |
-Related structure data
Related structure data | 42943MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 42 - 819 / Label seq-ID: 42 - 819
NCS oper: (Code: givenMatrix: (-0.999999982487, 4.20496311004E-5, -0.00018236526686), (-4.20581746387E-5, -0.999999998018, 4.68449132202E-5), (-0.000182363296687, 4.685258235E-5, 0.999999982274) ...NCS oper: (Code: given Matrix: (-0.999999982487, 4.20496311004E-5, -0.00018236526686), Vector: |
-Components
#1: Protein | Mass: 124098.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIDT1 / Plasmid: pEG BacMam C term 3C eGFP StrepII / Details (production host): Addgene # 160686 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) References: UniProt: Q9NXL6, UniProt: A0A5P9VSM8, NNS virus cap methyltransferase, RNA-directed RNA polymerase, GDP polyribonucleotidyltransferase |
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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 |
-Sample preparation
Component | Name: Human systemic RNAi defective transmembrane protein 1 (hSIDT1) Type: COMPLEX Details: Full length human SIDT1 expressed as a recombinant fusion protein with N-terminal GFP, in mammalian cells Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.1239 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293S GnTI- / Plasmid: pEG BacMam C term StrepII eGFP 3C | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: hSIDT1 in digitonin micelle, purified by Strep-Tactin affinity chromatography | ||||||||||||||||||||
Specimen support | Details: 15 mA current / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 17000 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3204173 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122683 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Atomic model building | Details: Made using Model angelo / Source name: Other / Type: in silico model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.76 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 5.21703157262E-13 Å |