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- EMDB-36785: SID1 transmembrane family member 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-36785
TitleSID1 transmembrane family member 1
Map data
Sample
  • Complex: human SID1 transmembrane family member 1 (SIDT1) homodimer
    • Protein or peptide: SID1 transmembrane family member 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / TRANSPORT PROTEIN
Function / homologyRNA 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsGuo H / Qi C / Lu Y / Yang H / Zhu Y / Sun F / Ji X
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: 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
DepositionJul 10, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_36785.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.62
Minimum - Maximum-3.3125386 - 4.570156
Average (Standard dev.)0.0065721306 (±0.12594412)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions164164164
Spacing164164164
CellA=B=C: 221.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : human SID1 transmembrane family member 1 (SIDT1) homodimer

EntireName: human SID1 transmembrane family member 1 (SIDT1) homodimer
Components
  • Complex: human SID1 transmembrane family member 1 (SIDT1) homodimer
    • Protein or peptide: SID1 transmembrane family member 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: human SID1 transmembrane family member 1 (SIDT1) homodimer

SupramoleculeName: human SID1 transmembrane family member 1 (SIDT1) homodimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SID1 transmembrane family member 1

MacromoleculeName: SID1 transmembrane family member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.771867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149089
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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