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- PDB-8jul: Cryo-EM structure of SIDT1 in complex with phosphatidic acid -

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Basic information

Entry
Database: PDB / ID: 8jul
TitleCryo-EM structure of SIDT1 in complex with phosphatidic acid
ComponentsSID1 transmembrane family member 1
KeywordsMEMBRANE PROTEIN / SID-1 transmembrane family member 1 / CREST family / phospholipase D / RNA uptake
Function / homology
Function and homology information


RNA transmembrane transporter activity / RNA transport / cholesterol binding / double-stranded RNA binding / lysosome / plasma membrane
Similarity search - Function
SID1 transmembrane family / dsRNA-gated channel SID-1
Similarity search - Domain/homology
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / SID1 transmembrane family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsSun, C.R. / Xu, D. / Li, Q. / Zhou, C.Z. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020202 China
CitationJournal: Cell Res / Year: 2024
Title: Human SIDT1 mediates dsRNA uptake via its phospholipase activity.
Authors: Cai-Rong Sun / Da Xu / Fengrui Yang / Zhuanghao Hou / Yuyao Luo / Chen-Yu Zhang / Ge Shan / Guangming Huang / Xuebiao Yao / Yuxing Chen / Qiong Li / Cong-Zhao Zhou /
History
DepositionJun 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SID1 transmembrane family member 1
B: SID1 transmembrane family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,0496
Polymers187,8472
Non-polymers1,2024
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein SID1 transmembrane family member 1


Mass: 93923.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIDT1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NXL6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C27H52O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of SIDT1 in complex with phosphatidic acid
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.16-3549 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 535389 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099924
ELECTRON MICROSCOPYf_angle_d0.77213492
ELECTRON MICROSCOPYf_dihedral_angle_d9.2425812
ELECTRON MICROSCOPYf_chiral_restr0.051554
ELECTRON MICROSCOPYf_plane_restr0.0071694

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