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- EMDB-36009: transport T2 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36009
Titletransport T2
Map data
Sample
  • Complex: T2
    • Protein or peptide: Green fluorescent protein (Fragment),SID1 transmembrane family member 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
Keywordstransport T2 / TRANSPORT PROTEIN
Function / homology
Function and homology information


nucleic acid transmembrane transporter activity / AP-1 adaptor complex binding / RNA transmembrane transporter activity / RNA transport / AP-2 adaptor complex binding / type B pancreatic cell development / regulation of insulin secretion involved in cellular response to glucose stimulus / type B pancreatic cell proliferation / RNA catabolic process / response to glucose ...nucleic acid transmembrane transporter activity / AP-1 adaptor complex binding / RNA transmembrane transporter activity / RNA transport / AP-2 adaptor complex binding / type B pancreatic cell development / regulation of insulin secretion involved in cellular response to glucose stimulus / type B pancreatic cell proliferation / RNA catabolic process / response to glucose / bioluminescence / generation of precursor metabolites and energy / cell morphogenesis / glucose homeostasis / double-stranded RNA binding / lysosome / lysosomal membrane / DNA binding / plasma membrane
Similarity search - Function
SID1 transmembrane family / dsRNA-gated channel SID-1 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / SID1 transmembrane family member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsJiang DH / Zhang JT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural insights into double-stranded RNA recognition and transport by SID-1.
Authors: Jiangtao Zhang / Chunhua Zhan / Junping Fan / Dian Wu / Ruixue Zhang / Di Wu / Xinyao Chen / Ying Lu / Ming Li / Min Lin / Jianke Gong / Daohua Jiang /
Abstract: RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA ...RNA uptake by cells is critical for RNA-mediated gene interference (RNAi) and RNA-based therapeutics. In Caenorhabditis elegans, RNAi is systemic as a result of SID-1-mediated double-stranded RNA (dsRNA) across cells. Despite the functional importance, the underlying mechanisms of dsRNA internalization by SID-1 remain elusive. Here we describe cryogenic electron microscopy structures of SID-1, SID-1-dsRNA complex and human SID-1 homologs SIDT1 and SIDT2, elucidating the structural basis of dsRNA recognition and import by SID-1. The homodimeric SID-1 homologs share conserved architecture, but only SID-1 possesses the molecular determinants within its extracellular domains for distinguishing dsRNA from single-stranded RNA and DNA. We show that the removal of the long intracellular loop between transmembrane helix 1 and 2 attenuates dsRNA uptake and systemic RNAi in vivo, suggesting a possible endocytic mechanism of SID-1-mediated dsRNA internalization. Our study provides mechanistic insights into dsRNA internalization by SID-1, which may facilitate the development of dsRNA applications based on SID-1.
History
DepositionApr 26, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36009.png

Downloads & links

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Map

FileDownload / File: emd_36009.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.328
Minimum - Maximum-4.972062 - 5.8865895
Average (Standard dev.)0.0037747608 (±0.11170302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36009_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36009_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T2

EntireName: T2
Components
  • Complex: T2
    • Protein or peptide: Green fluorescent protein (Fragment),SID1 transmembrane family member 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: T2

SupramoleculeName: T2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Green fluorescent protein (Fragment),SID1 transmembrane family me...

MacromoleculeName: Green fluorescent protein (Fragment),SID1 transmembrane family member 2
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 124.883797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS WSHPQFEKGG GSGGGSGGSA WSHPQFEKSK GEELFTGVVP ILVELDGDVN GHKFSVRGEG EGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD FFKSAMPEGY VQERTISFKD DGTYKTRAEV K FEGDTLVN ...String:
MYRMQLLSCI ALSLALVTNS WSHPQFEKGG GSGGGSGGSA WSHPQFEKSK GEELFTGVVP ILVELDGDVN GHKFSVRGEG EGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD FFKSAMPEGY VQERTISFKD DGTYKTRAEV K FEGDTLVN RIELKGIDFK EDGNILGHKL EYNFNSHNVY ITADKQKNGI KANFKIRHNV EDGSVQLADH YQQNTPIGDG PV LLPDNHY LSTQSVLSKD PNEKRDHMVL LEFVTAAGIT HGMDELEVLF QGPHLGVLGP KNVSQKDAEF ERTYVDEVNS ELV NIYTFN HTVTRNRTEG VRVSVNVLNK QKGAPLLFVV RQKEAVVSFQ VPLILRGMFQ RKYLYQKVER TLCQPPTKNE SEIQ FFYVD VSTLSPVNTT YQLRVSRMDD FVLRTGEQFS FNTTAAQPQY FKYEFPEGVD SVIVKVTSNK AFPCSVISIQ DVLCP VYDL DNNVAFIGMY QTMTKKAAIT VQRKDFPSNS FYVVVVVKTE DQACGGSLPF YPFAEDEPVD QGHRQKTLSV LVSQAV TSE AYVSGMLFCL GIFLSFYLLT VLLACWENWR QKKKTLLVAI DRACPESGHP RVLADSFPGS SPYEGYNYGS FENVSGS TD GLVDSAGTGD LSYGYQGRSF EPVGTRPRVD SMSSVEEDDY DTLTDIDSDK NVIRTKQYLY VADLARKDKR VLRKKYQI Y FWNIATIAVF YALPVVQLVI TYQTVVNVTG NQDICYYNFL CAHPLGNLSA FNNILSNLGY ILLGLLFLLI ILQREINHN RALLRNDLCA LECGIPKHFG LFYAMGTALM MEGLLSACYH VCPNYTNFQF DTSFMYMIAG LCMLKLYQKR HPDINASAYS AYACLAIVI FFSVLGVVFG KGNTAFWIVF SIIHIIATLL LSTQLYYMGR WKLDSGIFRR ILHVLYTDCI RQCSGPLYVD R MVLLVMGN VINWSLAAYG LIMRPNDFAS YLLAIGICNL LLYFAFYIIM KLRSGERIKL IPLLCIVCTS VVWGFALFFF FQ GLSTWQK TPAESREHNR DCILLDFFDD HDIWHFLSSI AMFGSFLVLL TLDDDLDTVQ RDKIYVF

UniProtKB: Green fluorescent protein, SID1 transmembrane family member 2

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104974

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