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- PDB-9l8o: Structure of SID-1 in complex with dsRNA (dodecameric form) -

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Basic information

Entry
Database: PDB / ID: 9l8o
TitleStructure of SID-1 in complex with dsRNA (dodecameric form)
Components
  • (RNA (24-mer)) x 2
  • Systemic RNA interference defective protein 1
KeywordsMEMBRANE PROTEIN/RNA / Membrane protein / Complex / MEMBRANE PROTEIN-RNA complex
Function / homology
Function and homology information


dsRNA transport / RNA transmembrane transporter activity / RNA transport / regulatory ncRNA-mediated post-transcriptional gene silencing / double-stranded RNA binding / lysosome / membrane / plasma membrane
Similarity search - Function
SID1 transmembrane family / dsRNA-gated channel SID-1
Similarity search - Domain/homology
RNA / RNA (> 10) / Systemic RNA interference defective protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsMurakoshi, S. / Kumazaki, K. / Kusakizako, T. / Nureki, O.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H05037 Japan
Japan Science and TechnologyJPMJCR20E2 Japan
Japan Agency for Medical Research and Development (AMED)JP19am01011115 Japan
CitationJournal: To Be Published
Title: Structural insights into SID1-mediated dsRNA uptake: A self-organizing endocytic mechanism
Authors: Takai, A. / Kumazaki, K. / Awazu, T. / Kambara, T. / Murakoshi, S. / Kato, T. / Hiraizumi, M. / Kise, Y. / Kusakizako, T. / Nishizawa, T. / Okada, T. / Nureki, O.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2347
Polymers93,0983
Non-polymers1,1354
Water00
1
A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules

A: Systemic RNA interference defective protein 1
C: RNA (24-mer)
D: RNA (24-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,130,80584
Polymers1,117,18036
Non-polymers13,62548
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.5, -0.866025), (0.866025, 0.5), (1)326.5347, -87.49471
3generate(-0.5, -0.866025), (0.866025, -0.5), (1)565.57471, 151.54529
4generate(-1), (-1), (1)478.07999, 478.07999
5generate(-0.5, 0.866025), (-0.866025, -0.5), (1)151.54529, 565.57471
6generate(0.5, 0.866025), (-0.866025, 0.5), (1)-87.49471, 326.5347
7generate(1), (-1), (-1)478.07999, 478.07999
8generate(0.5, 0.866025), (0.866025, -0.5), (-1)-87.49471, 151.54529, 478.07999
9generate(0.5, -0.866025), (-0.866025, -0.5), (-1)326.5347, 565.57471, 478.07999
10generate(-0.5, 0.866025), (0.866025, 0.5), (-1)151.54529, -87.49471, 478.07999
11generate(-0.5, -0.866025), (-0.866025, 0.5), (-1)565.57471, 326.5347, 478.07999
12generate(-1), (1), (-1)478.07999, 478.07999

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Components

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RNA chain , 2 types, 2 molecules CD

#2: RNA chain RNA (24-mer)


Mass: 3576.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (24-mer)


Mass: 3322.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Non-polymers , 2 types, 2 molecules A

#1: Protein Systemic RNA interference defective protein 1 / Systemic RNAi enabling protein


Mass: 86199.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: sid-1, rde-7, rsd-8, C04F5.1 / Production host: Homo sapiens (human) / References: UniProt: Q9GZC8
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Sugars , 2 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
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: SID-1 in complex with dsRNA / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.86 MDa / Experimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10734
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
7Coot0.9.6model fitting
9Servalcat0.4.88model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1772453
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52278 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: dsRNA-bound SID-1 model in our accompanying PDB entry
Source name: Other / Type: experimental model
RefinementResolution: 3.99→3.99 Å / Cor.coef. Fo:Fc: 0.931 / WRfactor Rwork: 0.381 / SU B: 41.873 / SU ML: 0.582 / Average fsc overall: 0.7802 / Average fsc work: 0.7802 / ESU R: 0.186
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3808 379645 -
all0.381 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 257.033 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0150.0135777
ELECTRON MICROSCOPYr_bond_other_d00.0175233
ELECTRON MICROSCOPYr_angle_refined_deg1.7021.6177902
ELECTRON MICROSCOPYr_angle_other_deg1.3321.64712058
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.6835.829736
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.64822.099243
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.89315894
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.4651524
ELECTRON MICROSCOPYr_chiral_restr0.0910.2817
ELECTRON MICROSCOPYr_gen_planes_refined0.010.025988
ELECTRON MICROSCOPYr_gen_planes_other0.0040.021337
ELECTRON MICROSCOPYr_nbd_refined0.180.21682
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1220.28316
ELECTRON MICROSCOPYr_nbtor_refined0.1510.24940
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0660.25288
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1340.2158
ELECTRON MICROSCOPYr_symmetry_nbd_refined0.1940.215
ELECTRON MICROSCOPYr_nbd_other0.5280.265
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_refined0.2730.22
ELECTRON MICROSCOPYr_paralell_plane_angle_deg12.321639
ELECTRON MICROSCOPYr_mcbond_it14.50928.3542518
ELECTRON MICROSCOPYr_mcbond_other14.51228.3482517
ELECTRON MICROSCOPYr_mcangle_it24.18142.4953137
ELECTRON MICROSCOPYr_mcangle_other24.17742.5023138
ELECTRON MICROSCOPYr_scbond_it12.66326.1773259
ELECTRON MICROSCOPYr_scbond_other12.66426.1783258
ELECTRON MICROSCOPYr_scangle_it22.12939.0574765
ELECTRON MICROSCOPYr_scangle_other22.12739.0564766
ELECTRON MICROSCOPYr_lrange_it44.071534.79323406
ELECTRON MICROSCOPYr_lrange_other44.072534.80923405
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.9-4.0010.842281390.842281390.5630.842
4.001-4.1110.511272540.511272540.6540.511
4.111-4.230.417269090.417269090.7330.417
4.23-4.360.381255670.381255670.7730.381
4.36-4.5030.371251180.371251180.7980.371
4.503-4.6610.372243360.372243360.8060.372
4.661-4.8370.374233200.374233200.8010.374
4.837-5.0350.377224580.377224580.8370.377
5.035-5.2590.385216710.385216710.8350.385
5.259-5.5150.393206770.393206770.8170.393
5.515-5.8130.385196710.385196710.8110.385
5.813-6.1660.372185480.372185480.8130.372
6.166-6.5910.369173710.369173710.8090.369
6.591-7.1190.375162840.375162840.8150.375
7.119-7.7990.357148900.357148900.8340.357
7.799-8.7190.392134230.392134230.8110.392
8.719-10.0660.364119180.364119180.850.364
10.066-12.3260.369100200.369100200.8490.369
12.326-17.4210.3477980.3477980.8590.34
17.421-351.920.35642720.35642720.9250.356

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