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- EMDB-0360: S. cerevisiae spliceosomal E complex (UBC4) -

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Basic information

Entry
Database: EMDB / ID: EMD-0360
TitleS. cerevisiae spliceosomal E complex (UBC4)
Map data
SampleSaccharomyces cerevisiae spliceosomal E complex (EBC4)
  • (U1 small nuclear ribonucleoprotein ...) x 5
  • (Pre-mRNA-processing ...) x 2
  • Protein NAM8
  • 56 kDa U1 small nuclear ribonucleoprotein component
  • Protein LUC7
  • Small nuclear ribonucleoprotein-associated protein B
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (nucleic-acidNucleic acid) x 2
  • (Nuclear cap-binding protein ...) x 2
  • ligand
Function / homology
Function and homology information


Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Processing of Intronless Pre-mRNAs / mRNA Capping / RNA Polymerase II Pre-transcription Events / Formation of the Early Elongation Complex / nuclear cap binding complex / positive regulation of RNA binding / mRNA splice site selection / splicing factor binding ...Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Processing of Intronless Pre-mRNAs / mRNA Capping / RNA Polymerase II Pre-transcription Events / Formation of the Early Elongation Complex / nuclear cap binding complex / positive regulation of RNA binding / mRNA splice site selection / splicing factor binding / positive regulation of mRNA splicing, via spliceosome / RNA cap binding / pICln-Sm protein complex / mRNA 5'-splice site recognition / U4 snRNP / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / mRNA cap binding complex / pre-mRNA 5'-splice site binding / mRNA cis splicing, via spliceosome / commitment complex / U12-type spliceosomal complex / U2 snRNP / small nucleolar ribonucleoprotein complex / U5 snRNP / spliceosomal snRNP assembly / U2-type prespliceosome / P granule / U1 snRNP / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / poly(U) RNA binding / mRNA transport / 7-methylguanosine mRNA capping / response to osmotic stress / catalytic step 2 spliceosome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / polysome / mRNA splicing, via spliceosome / mRNA binding / perinuclear region of cytoplasm / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Sm-like protein Lsm6/SmF / MIF4G-like, type 1 / Nuclear cap-binding protein subunit 2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein E / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein C / Armadillo-type fold / MIF4G-like domain superfamily / MIF4G-like, type 2 ...Sm-like protein Lsm6/SmF / MIF4G-like, type 1 / Nuclear cap-binding protein subunit 2 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein E / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein C / Armadillo-type fold / MIF4G-like domain superfamily / MIF4G-like, type 2 / U1-C, C2H2-type zinc finger / Small nuclear ribonucleoprotein Sm D2 / Nucleotide-binding alpha-beta plait domain superfamily / Tetratricopeptide-like helical domain superfamily / LSM domain superfamily / Luc7-related / MIF4G-like, type 3 / Matrin/U1-C-like, C2H2-type zinc finger / HAT (Half-A-TPR) repeat / FF domain / Nuclear cap-binding protein subunit 1 / Small nuclear ribonucleoprotein G / WW/rsp5/WWP domain signature. / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / MIF4G like / MIF4G like / U1 zinc finger / LUC7 N_terminus / MIF4G domain / FF domain / LSM domain / WW domain / U1 small nuclear ribonucleoprotein 70kDa / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-processing factor Prp40 / FF domain superfamily / Zinc finger C2H2 superfamily / WW domain superfamily / RNA-binding domain superfamily / NCBP2, RNA recognition motif / snRNP70, RNA recognition motif / Small nuclear ribonucleoprotein F / PWI domain / WW domain / LSM domain, eukaryotic/archaea-type / Eukaryotic RNA Recognition Motif (RRM) profile. / FF domain profile. / Zinc finger matrin-type profile. / Matrin/U1-C, C2H2-type zinc finger / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / WW/rsp5/WWP domain profile. / RNA recognition motif domain
U1 small nuclear ribonucleoprotein 70 kDa homolog / Nuclear cap-binding protein subunit 2 / Protein LUC7 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein C / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein component PRP42 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein-associated protein B / Protein NAM8 ...U1 small nuclear ribonucleoprotein 70 kDa homolog / Nuclear cap-binding protein subunit 2 / Protein LUC7 / Small nuclear ribonucleoprotein Sm D2 / U1 small nuclear ribonucleoprotein C / 56 kDa U1 small nuclear ribonucleoprotein component / U1 small nuclear ribonucleoprotein component PRP42 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein-associated protein B / Protein NAM8 / Small nuclear ribonucleoprotein F / U1 small nuclear ribonucleoprotein component SNU71 / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein G / Pre-mRNA-processing factor 39 / Nuclear cap-binding protein complex subunit 1 / Pre-mRNA-processing protein PRP40 / U1 small nuclear ribonucleoprotein A / Small nuclear ribonucleoprotein E
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu S / Li X / Zhou ZH / Zhao R
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteGM126157 United States
National Institutes of Health/National Human Genome Research InstituteGM071940 United States
National Institutes of Health/National Human Genome Research InstituteGM114178 United States
National Institutes of Health/National Human Genome Research InstituteAI094386 United States
CitationJournal: Nature / Year: 2019
Title: A unified mechanism for intron and exon definition and back-splicing.
Authors: Xueni Li / Shiheng Liu / Lingdi Zhang / Aaron Issaian / Ryan C Hill / Sara Espinosa / Shasha Shi / Yanxiang Cui / Kalli Kappel / Rhiju Das / Kirk C Hansen / Z Hong Zhou / Rui Zhao /
Abstract: The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E ...The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes.
Validation ReportPDB-ID: 6n7p

SummaryFull reportAbout validation report
History
DepositionNov 27, 2018-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n7p
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0360.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 384 pix.
= 522.24 Å
1.36 Å/pix.
x 384 pix.
= 522.24 Å
1.36 Å/pix.
x 384 pix.
= 522.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.20593081 - 0.37101442
Average (Standard dev.)-0.00004524245 (±0.0076556755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 522.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z522.240522.240522.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2060.371-0.000

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Supplemental data

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Sample components

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Entire Saccharomyces cerevisiae spliceosomal E complex (EBC4)

EntireName: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
Number of components: 23

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Component #1: protein, Saccharomyces cerevisiae spliceosomal E complex (EBC4)

ProteinName: Saccharomyces cerevisiae spliceosomal E complex (EBC4)
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, U1 small nuclear ribonucleoprotein 70 kDa homolog

ProteinName: U1 small nuclear ribonucleoprotein 70 kDa homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.506148 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: protein, U1 small nuclear ribonucleoprotein C

ProteinName: U1 small nuclear ribonucleoprotein C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.106016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, U1 small nuclear ribonucleoprotein A

ProteinName: U1 small nuclear ribonucleoprotein A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.413961 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #5: protein, U1 small nuclear ribonucleoprotein component PRP42

ProteinName: U1 small nuclear ribonucleoprotein component PRP42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.22202 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, Pre-mRNA-processing factor 39

ProteinName: Pre-mRNA-processing factor 39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.834742 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, Protein NAM8

ProteinName: Protein NAM8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.01084 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, 56 kDa U1 small nuclear ribonucleoprotein component

ProteinName: 56 kDa U1 small nuclear ribonucleoprotein component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.575277 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, U1 small nuclear ribonucleoprotein component SNU71,U1 sm...

ProteinName: U1 small nuclear ribonucleoprotein component SNU71,U1 small nuclear ribonucleoprotein component SNU71,Snu71
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.48532 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Protein LUC7

ProteinName: Protein LUC7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.245885 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, Pre-mRNA-processing protein PRP40

ProteinName: Pre-mRNA-processing protein PRP40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.176016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Small nuclear ribonucleoprotein-associated protein B

ProteinName: Small nuclear ribonucleoprotein-associated protein B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.42699 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, Small nuclear ribonucleoprotein Sm D1

ProteinName: Small nuclear ribonucleoprotein Sm D1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.296798 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, Small nuclear ribonucleoprotein Sm D2

ProteinName: Small nuclear ribonucleoprotein Sm D2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.876066 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, Small nuclear ribonucleoprotein Sm D3

ProteinName: Small nuclear ribonucleoprotein Sm D3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.240139 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, Small nuclear ribonucleoprotein E

ProteinName: Small nuclear ribonucleoprotein E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.385098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, Small nuclear ribonucleoprotein F

ProteinName: Small nuclear ribonucleoprotein F / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.669945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, Small nuclear ribonucleoprotein G

ProteinName: Small nuclear ribonucleoprotein G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.490809 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: nucleic-acid, U1 snRNA

nucleic acidName: U1 snRNAU1 spliceosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUACUUACCU UAAGAUAUCA GAGGAGAUCA AGAAGUCCUA CUGAUCAAAC AUGCGCUUCC AAUAGUAGAA GGACGUUAAG CAUUUAUCAU UGAACUAUAA UUGUUCAUUG AAGUCAUUGA UGCAAACUCC UUGGUCACAC ACACAUACGG CGCGGAAGGC GUGUUUGCUG ACGUUUCCAU UCCCUUGUUU CAAUCAUUGG UUAAUCCCUU GAUUCCUUUG GGGAUUUUUG GGUUAAACUG AUUUUUGGGG CCCUUUGUUU CUUCUGCCUG GAGAAGUUUG ACACCAAAUU CAAAUUGGUG UUAGGGGAGC UGGGGCCUUU CAAAAGAGAG CUUUGUAGAG GCAUUCUUUU UGACUACUUU UCUCUAGCGU GCCAUUUUAG UUUUUGACGG CAGAUUCGAA UGAACUUAAG UUUAUGAUGA AGGUAUGGCU GUUGAGAUUA UUUGGUCGGG AUUGUAGUUU GAAGAUGUGC UCUUUUGAGC AGUCUCAACU UUGCUCGUUC CCGUUAUGGG AAAAAUUUUG GAAGGUCUUG GUAGGAACGG GUGGAUCUUA UAAUUUUUGA UUUAUUUU
MassTheoretical: 182.114516 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: nucleic-acid, UBC4 pre-mRNA

nucleic acidName: UBC4 pre-mRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGAACUAAG UGAUCUAGAA AGGUAUGUCU AAAGUUAUGG CCACGUUUCA AAUGCGUGCU UUUUUUUUAA AACUUAUGCU CUUAUUUACU AACAAAAUCA ACAUGCUAUU GAACUAGAGA UCCACCUACU UCAUGUUCAG CCGGUCCAGG AUCCGAUAUC CGUACACCAU CAGGGUACGA GCUAGCCCAU GGCGUACACC AUCAGGGUAC GACUAGUAGA UCUCGUACAC CAUCAGGGUA CGGAAUUCUC UAG
MassTheoretical: 81.030773 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #21: protein, Nuclear cap-binding protein complex subunit 1

ProteinName: Nuclear cap-binding protein complex subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.115047 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #22: protein, Nuclear cap-binding protein subunit 2

ProteinName: Nuclear cap-binding protein subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.803467 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.9
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 124825
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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