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- EMDB-8124: Structure of the yeast Kluyveromyces lactis small ribosomal subun... -

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Basic information

Entry
Database: EMDB / ID: 8124
TitleStructure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.
Map data
SampleKluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES:
(Ribosomal protein ...) x 33 / (nucleic-acidNucleic acid) x 2 / (ligand) x 2
Function / homology40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S11 superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily ...40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S11 superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / RNA-binding S4 domain superfamily / 50S ribosomal protein L30e-like / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S21e superfamily / S27a-like superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ubiquitin-like domain superfamily / Ribosomal protein S28e conserved site / Ubiquitin family / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S9, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / Ribosomal protein S19 / Ribosomal protein S14p/S29e / Ribosomal protein S17e, conserved site / Ribosomal protein S12 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S17 signature. / S25 ribosomal protein / Ubiquitin domain signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S3 signature. / Ribosomal protein S6e signature. / Ribosomal protein S5 signature. / Ribosomal protein S19e signature. / Ribosomal protein S4 signature. / Plectin/S10 domain / Ribosomal protein S27 / Ribosomal protein S15 / Ribosomal S17 / Ribosomal protein S2 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10p/S20e / Ribosomal protein S17 / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / KOW motif / Ribosomal family S4e / Ribosomal protein S27a / Ribosomal S3Ae family / Ribosomal protein S19e / Ribosomal protein S6e / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Function and homology information
SourceKluyveromyces lacti (yeast) / Kluyveromyces lactis (yeast)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsMurray J / Savva CG
CitationJournal: Elife / Year: 2016
Title: Structural characterization of ribosome recruitment and translocation by type IV IRES.
Authors: Jason Murray / Christos G Savva / Byung-Sik Shin / Thomas E Dever / V Ramakrishnan / Israel S Fernández
Validation ReportPDB-ID: 5it9

SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2016 / Header (metadata) release: May 18, 2016 / Map release: May 18, 2016 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5it9
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8124.map.gz (map file in CCP4 format, 87809 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
1.34 Å/pix.
= 375.2 Å
280 pix
1.34 Å/pix.
= 375.2 Å
280 pix
1.34 Å/pix.
= 375.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density
Contour Level:0.1 (by author), 0.14 (movie #1):
Minimum - Maximum-0.64123625 - 0.9734524
Average (Standard dev.)-9.4434596E-5 (0.041961007)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin000
Limit279279279
Spacing280280280
CellA=B=C: 375.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z375.200375.200375.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.6410.973-0.000

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Supplemental data

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Mask #1

Fileemd_8124_msk_1.map ( map file in CCP4 format, 87809 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsNone
Space group number1

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Mask #1~

Fileemd_8124_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Kluyveromyces lactis small ribosomal subunit in complex with the ...

EntireName: Kluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES
Number of components: 38
MassTheoretical: 2 MDa

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Component #1: protein, Kluyveromyces lactis small ribosomal subunit in complex ...

ProteinName: Kluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES
Recombinant expression: No
MassTheoretical: 2 MDa
SourceSpecies: Kluyveromyces lacti (yeast)

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Component #2: protein, Ribosomal protein uS2

ProteinName: Ribosomal protein uS2 / Recombinant expression: No
MassTheoretical: 22.882172 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #3: protein, Ribosomal protein eS1

ProteinName: Ribosomal protein eS1 / Recombinant expression: No
MassTheoretical: 24.488287 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #4: protein, Ribosomal protein uS5

ProteinName: Ribosomal protein uS5 / Recombinant expression: No
MassTheoretical: 23.162922 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #5: protein, Ribosomal protein uS3

ProteinName: Ribosomal protein uS3 / Recombinant expression: No
MassTheoretical: 24.830895 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #6: protein, Ribosomal protein eS4

ProteinName: Ribosomal protein eS4 / Recombinant expression: No
MassTheoretical: 29.486312 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #7: protein, Ribosomal protein uS7

ProteinName: Ribosomal protein uS7 / Recombinant expression: No
MassTheoretical: 22.912369 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #8: protein, Ribosomal protein eS6

ProteinName: Ribosomal protein eS6 / Recombinant expression: No
MassTheoretical: 25.810977 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #9: protein, Ribosomal protein eS7

ProteinName: Ribosomal protein eS7 / Recombinant expression: No
MassTheoretical: 21.03357 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #10: protein, Ribosomal protein eS8

ProteinName: Ribosomal protein eS8 / Recombinant expression: No
MassTheoretical: 22.511531 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #11: protein, Ribosomal protein uS4

ProteinName: Ribosomal protein uS4 / Recombinant expression: No
MassTheoretical: 20.882344 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #12: protein, Ribosomal protein eS10

ProteinName: Ribosomal protein eS10 / Recombinant expression: No
MassTheoretical: 11.423085 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #13: protein, Ribosomal protein uS17

ProteinName: Ribosomal protein uS17 / Recombinant expression: No
MassTheoretical: 17.712734 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #14: protein, Ribosomal protein eS12

ProteinName: Ribosomal protein eS12 / Recombinant expression: No
MassTheoretical: 13.124912 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #15: protein, Ribosomal protein uS15

ProteinName: Ribosomal protein uS15 / Recombinant expression: No
MassTheoretical: 16.858678 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #16: protein, Ribosomal protein uS14

ProteinName: Ribosomal protein uS14 / Recombinant expression: No
MassTheoretical: 13.458439 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #17: protein, Ribosomal protein uS19

ProteinName: Ribosomal protein uS19 / Recombinant expression: No
MassTheoretical: 14.055573 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #18: protein, Ribosomal protein uS9

ProteinName: Ribosomal protein uS9 / Recombinant expression: No
MassTheoretical: 15.656257 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #19: protein, Ribosomal protein eS17

ProteinName: Ribosomal protein eS17 / Recombinant expression: No
MassTheoretical: 14.72898 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #20: protein, Ribosomal protein uS13

ProteinName: Ribosomal protein uS13 / Recombinant expression: No
MassTheoretical: 16.953404 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #21: protein, Ribosomal protein eS19

ProteinName: Ribosomal protein eS19 / Recombinant expression: No
MassTheoretical: 15.747814 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #22: protein, Ribosomal protein uS10

ProteinName: Ribosomal protein uS10 / Recombinant expression: No
MassTheoretical: 12.032146 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #23: protein, Ribosomal protein eS21

ProteinName: Ribosomal protein eS21 / Recombinant expression: No
MassTheoretical: 9.797949 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #24: protein, Ribosomal protein uS8

ProteinName: Ribosomal protein uS8 / Recombinant expression: No
MassTheoretical: 14.513846 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #25: protein, Ribosomal protein uS21

ProteinName: Ribosomal protein uS21 / Recombinant expression: No
MassTheoretical: 16.047897 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #26: protein, Ribosomal protein eS24

ProteinName: Ribosomal protein eS24 / Recombinant expression: No
MassTheoretical: 15.063354 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #27: protein, Ribosomal protein eS25

ProteinName: Ribosomal protein eS25 / Recombinant expression: No
MassTheoretical: 7.939246 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #28: protein, Ribosomal protein eS26

ProteinName: Ribosomal protein eS26 / Recombinant expression: No
MassTheoretical: 11.454568 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #29: protein, Ribosomal protein eS27

ProteinName: Ribosomal protein eS27 / Recombinant expression: No
MassTheoretical: 8.884362 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #30: protein, Ribosomal protein eS28

ProteinName: Ribosomal protein eS28 / Recombinant expression: No
MassTheoretical: 7.073256 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #31: protein, Ribosomal protein eS29

ProteinName: Ribosomal protein eS29 / Recombinant expression: No
MassTheoretical: 6.322149 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #32: protein, Ribosomal protein eS30

ProteinName: Ribosomal protein eS30 / Recombinant expression: No
MassTheoretical: 6.329429 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #33: protein, Ribosomal protein eS31

ProteinName: Ribosomal protein eS31 / Recombinant expression: No
MassTheoretical: 7.958424 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #34: protein, Ribosomal protein RACK1

ProteinName: Ribosomal protein RACK1 / Recombinant expression: No
MassTheoretical: 35.612676 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #35: nucleic-acid, 18S ribosomal RNA

Nucleic-acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGAUAUCUG UGGUAAUUCU AGAGCUAAUA CAUGCUUAAA AUCUCGACCC UUUGGAAGAG AUGUAUUUAU UAGAUAAAAA AUCAAUGUCU UCGGACUCCU UGAUGAUUCA UAAUAACUUU UCGAAUCGCA UGGCCUUGUG CUGGCGAUGG UUCAUUCAAA UUUCUGCCCU AUCAACUUUC GAUGGUAGGA UAGUGGCCUA CCAUGGUUUC AACGGGUAAC GGGGAAUAAG GGUUCGAUUC CGGAGAGGGA GCCUGAGAAA CGGCUACCAC AUCCAAGGAA GGCAGCAGGC GCGCAAAUUA CCCAAUCCUA AUUCAGGGAG GUAGUGACAA UAAAUAACGA UACAGGGCCC AUUCGGGUCU UGUAAUUGGA AUGAGUACAA UGUAAAUACC UUAACGAGGA ACAACUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA GUAGCGUAUA UUAAAGUUGU UGCAGUUAAA AAGCUCGUAG UUGAACUUUG GGUCUGGUUG UCCGGUCGGU UUUUCAACCG GAUCUUUCCU UCUGGCUAAC CUGUACUCCU UGUGGGUGCA GGCGAACCAG GACUUUUACU UUGAAAAAAU UAGAGUGUUC AAAGCAGGCG AAAGCUCGAA UAUAUUAGCA UGGAAUAAUG GAAUAGGACG UUUGGUUCUA UUUUGUUGGU UUCUAGGACC AUCGUAAUGA UUAAUAGGGA CGGUCGGGGG CAUCAGUAUU CAAUUGUCAG AGGUGAAAUU CUUGGAUUUA UUGAAGACUA ACUACUGCGA AAGCAUUUGC CAAGGACGUU UUCAUUAAUC AAGAACGAAA GUUAGGGGAU CGAAGAUGAU CAGAUACCGU CGUAGUCUUA ACCAUAAACU AUGCCGACUA GGGAUCGGGU GGUGUUUUUC UUAUGACCCA CUCGGCACCU UACGAGAAAU CAAAGUCUUU GGGUUCUGGG GGGAGUAUGG UCGCAAGGCU GAAACUUAAA GGAAUUGACG GAAGGGCACC ACCAGGAGUG GAGCCUGCGG CUUAAUUUGA CUCAACACGG GGAAACUCAC CAGGUCCAGA CACAAUAAGG AUUGACAGAU UGAGAGCUCU UUCUUGAUUU UGUGGGUGGU GGUGCAUGGC CGUUCUUAGU UGGUGGAGUG AUUUGUCUGC UUAAUUGCGA UAACGAACGA GACCUUAACC UACUAAAUAG GGUUGCUGGC ACUUGCCGGU UGACUCUUCU UAGAGGGACU AUCGGUUUCA AGCCGAUGGA AGUUUGAGGC AAUAACAGGU CUGUGAUGCC CUUAGACGUU CUGGGCCGCA CGCGCGCUAC ACUGACGGAG CCAGCGAGUA CAACCUUGGC CGAGAGGUCU GGGUAAUCUU GUGAAACUCC GUCGUGCUGG GGAUAGAGCA UUGUAAUUAU UGCUCUUCAA CGAGGAAUUC CUAGUAAGCG CAAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUUUGCUUAG AGAAGGGGGC AACUCCAUCU CAGAGCGAAG AAUCUGGUCA AACUUGGUCA UUUAGAGGAA CUAAAAGUCG UAACAAGGUU UCCGUAGGUG AACCUGCGGA AGGAUCAUUA
MassTheoretical: 573.508938 kDa
SourceSpecies: Kluyveromyces lactis (yeast)

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Component #36: nucleic-acid, Cricket paralysis virus IRES RNA

Nucleic-acidName: Cricket paralysis virus IRES RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAAAAUGUGA UCUUGCUUGU AAAUACAAUU UUGAGAGGUU AAUAAAUUAC AAGUAGUGCU AUUUUUGUAU UUAGGUUAGC UAUUUAGCUU UACGUUCCAG GAUGCCUAGU GGCAGCCCCA CAAUAUCCAG GAAGCCCUCU CUGCGGCUUU UCAGAUUAGG UAGUCGAAAA ACCUAAGAAA UUUACCUGCU AC
MassTheoretical: 61.462207 kDa

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Component #37: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 80 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #38: 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: 6.5
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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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: 25 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 54481
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 3.8 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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