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- EMDB-36792: SID1 transmembrane family member 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-36792
TitleSID1 transmembrane family member 1
Map data
Sample
  • Complex: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD focused refinement
    • Protein or peptide: SID1 transmembrane family member 1
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: 3.53 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 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36792.png

Downloads & links

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Map

FileDownload / File: emd_36792.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 164 pix.
= 221.4 Å		1.35 Å/pix.
x 164 pix.
= 221.4 Å		1.35 Å/pix.
x 164 pix.
= 221.4 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-2.0098941 - 3.092407
Average (Standard dev.)0.0058872392 (±0.10221447)
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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Half map: #2

Fileemd_36792_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36792_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD f...

EntireName: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD focused refinement
Components
  • Complex: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD focused refinement
    • Protein or peptide: SID1 transmembrane family member 1

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Supramolecule #1: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD f...

SupramoleculeName: human SID1 transmembrane family member 1 (SIDT1) homodimer, TMD focused refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 58.291754 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: IKESVYVKSS LFSVFIFLSF YLGCLLVGFV HYLRFQRKSI DGSFGSNDGS GNMVASHPIA ASTPEPDIES DKNIIRTKMF LYLSDLSRK DRRIVSKKYK IYFWNIITIA VFYALPVIQL VITYQTVVNV TGNQDICYYN FLCAHPLGVL SAFNNILSNL G HVLLGFLF ...String:
IKESVYVKSS LFSVFIFLSF YLGCLLVGFV HYLRFQRKSI DGSFGSNDGS GNMVASHPIA ASTPEPDIES DKNIIRTKMF LYLSDLSRK DRRIVSKKYK IYFWNIITIA VFYALPVIQL VITYQTVVNV TGNQDICYYN FLCAHPLGVL SAFNNILSNL G HVLLGFLF LLIVLRRDIL HRRALEAKDI FAVEYGIPKH FGLFYAMGIA LMMEGVLSAC YHVCPNYSNF QFDTSFMYMI AG LCMLKLY QTRHPDINAS AYSAYASFAV VIMVTVLGVV FGKNDVWFWV IFSAIHVLAS LALSTQIYYM GRFKIDLGIF RRA AMVFYT DCIQQCSRPL YMDRMVLLVV GNLVNWSFAL FGLIYRPRDF ASYMLGIFIC NLLLYLAFYI IMKLRSSEKV LPVP LFCIV ATAVMWAAAL YFFFQNLSSW EGTPAESREK NRECILLDFF DDHDIWHFLS ATALFFSFLV LLTLDDDLDV VRRDQ IPVF DYKDHDGDYK DHDIDYKDDD DK

UniProtKB: SID1 transmembrane family member 1

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81463
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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