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- EMDB-37696: Cryo-EM structure of human SIDT1 protein with C2 symmetry at neut... -

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Basic information

Entry
Database: EMDB / ID: EMD-37696
TitleCryo-EM structure of human SIDT1 protein with C2 symmetry at neutral pH
Map data
Sample
  • Complex: Ternary complex of SIDT1 in complex with unknown lipids
    • Protein or peptide: SID1 transmembrane family member 1
  • Ligand: ZINC ION
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: OLEIC ACID
  • Ligand: OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
  • Ligand: water
KeywordsCeramidase / putative RNA and cholesterol transport protein / HYDROLASE
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: 2.66 Å
AuthorsLiu W / Tang M / Wang J / Zhang X / Wu S / Ru H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371344 China
CitationJournal: Cell Discov / Year: 2024
Title: Structural insights into cholesterol transport and hydrolase activity of a putative human RNA transport protein SIDT1.
Authors: Wenxia Liu / Mengyuan Tang / Jiening Wang / Fangfang Wang / Gaojie Song / Xiaokang Zhang / Shan Wu / Heng Ru /
History
DepositionOct 7, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37696.png

Downloads & links

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Map

FileDownload / File: emd_37696.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.851 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6246399 - 1.0003408
Average (Standard dev.)0.000203545 (±0.01796376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37696_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_37696_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 : Ternary complex of SIDT1 in complex with unknown lipids

EntireName: Ternary complex of SIDT1 in complex with unknown lipids
Components
  • Complex: Ternary complex of SIDT1 in complex with unknown lipids
    • Protein or peptide: SID1 transmembrane family member 1
  • Ligand: ZINC ION
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: OLEIC ACID
  • Ligand: OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
  • Ligand: water

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Supramolecule #1: Ternary complex of SIDT1 in complex with unknown lipids

SupramoleculeName: Ternary complex of SIDT1 in complex with unknown lipids
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: 99.695211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 FKIDVSDTDL GIFRRAAMVF YTDCIQQCSR PLYMDRMVLL VVGNLVNWSF ALFGLIYRPR DFASYMLG I FICNLLLYLA FYIIMKLRSS EKVLPVPLFC IVATAVMWAA ALYFFFQNLS SWEGTPAESR EKNRECILLD FFDDHDIWH FLSATALFFS FLVLLTLDDD LDVVRRDQIP VFSRENLYFQ GSGWSHPQFE KGGGSGGGSG GSAWSHPQFE KGSDYKDDDD K

UniProtKB: SID1 transmembrane family member 1

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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 #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 15 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #7: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 7 / Number of copies: 2 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID / Oleic acid

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Macromolecule #8: OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE

MacromoleculeName: OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
type: ligand / ID: 8 / Number of copies: 2 / Formula: SPL
Molecular weightTheoretical: 425.688 Da
Chemical component information

ChemComp-SPL:
OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE / Ceramide

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 1.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.52 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 503286
FSC plot (resolution estimation)

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