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- EMDB-8362: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase L... -

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Basic information

Entry
Database: EMDB / ID: 8362
TitleNmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex
Sample60S in complex with Nmd3, Lsg1, and Tif6
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map dataNmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex
Methodsingle particle reconstruction, at 3.1 Å resolution
AuthorsMalyutin AG / Musalgaonkar S / Patchett S / Frank J / Johnson AW
CitationEMBO J., 2017, 36, 854-868

EMBO J., 2017, 36, 854-868 Yorodumi Papers
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
Andrey G Malyutin / Sharmishtha Musalgaonkar / Stephanie Patchett / Joachim Frank / Arlen W Johnson

Validation ReportPDB-ID: 5t62

SummaryFull reportAbout validation report
DateDeposition: Sep 27, 2016 / Header (metadata) release: Dec 28, 2016 / Map release: Feb 8, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5t62
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_8362.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.09 Å/pix.
= 392.4 Å
360 pix
1.09 Å/pix.
= 392.4 Å
360 pix
1.09 Å/pix.
= 392.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider package.

Voxel size
XYZ
EMDB info.1.261.261.26
CCP4 map header1.091.091.09
EM Navigator Movie #11.091.091.09
Density
Contour Level:0.0225 (by emdb), 0.05 (movie #1):
Minimum - Maximum-0.024771579 - 0.07995617
Average (Standard dev.)0.0010139983 (0.005039435)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 403.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z392.400392.400392.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2330.4110.001

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Supplemental data

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Sample components

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Entire 60S in complex with Nmd3, Lsg1, and Tif6

EntireName: 60S in complex with Nmd3, Lsg1, and Tif6 / Number of components: 53

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Component #1: protein, 60S in complex with Nmd3, Lsg1, and Tif6

ProteinName: 60S in complex with Nmd3, Lsg1, and Tif6 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #2: protein, 60S-Nmd3-Tif6-Lsg1 complex with focus on Nmd3

ProteinName: 60S-Nmd3-Tif6-Lsg1 complex with focus on Nmd3
Details: This map was acquired by combining 60S-Nmd3 and 60S-Nmd3-Tif6-Lsg1 datasets to increase the number of particles containing 60S-Nmd3 in closed conformation.
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #3: protein, Eukaryotic translation initiation factor 6

ProteinName: Eukaryotic translation initiation factor 6 / Recombinant expression: No
MassTheoretical: 28.597959 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Vector: pAJ3283 / Strain: ATCC 204508 / S288c

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Component #4: nucleic-acid, Saccharomyces cerevisiae S288c 35S pre-ribosomal RN...

Nucleic-acidName: Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG GGGCCGUUCC UUGUCUAUGU UCCUUGGAAC AGGACGUCAU AGAGGGUGAG AAUCCCGUGU GGCGAGGAGU GCGGUUCUUU GUAAAGUGCC UUCGAAGAGU CGAGUUGUUU GGGAAUGCAG CUCUAAGUGG GUGGUAAAUU CCAUCUAAAG CUAAAUAUUG GCGAGAGACC GAUAGCGAAC AAGUACAGUG AUGGAAAGAU GAAAAGAACU UUGAAAAGAG AGUGAAAAAG UACGUGAAAU UGUUGAAAGG GAAGGGCAUU UGAUCAGACA UGGUGUUUUG UGCCCUCUGC UCCUUGUGGG UAGGGGAAUC UCGCAUUUCA CUGGGCCAGC AUCAGUUUUG GUGGCAGGAU AAAUCCAUAG GAAUGUAGCU UGCCUCGGUA AGUAUUAUAG CCUGUGGGAA UACUGCCAGC UGGGACUGAG GACUGCGACG UAAGUCAAGG AUGCUGGCAU AAUGGUUAUA UGCCGCCCGU CUUGAAACAC GGACCAAGGA GUCUAACGUC UAUGCGAGUG UUUGGGUGUA AAACCCAUAC GCGUAAUGAA AGUGAACGUA GGUUGGGGCC UCGCAAGAGG UGCACAAUCG ACCGAUCCUG AUGUCUUCGG AUGGAUUUGA GUAAGAGCAU AGCUGUUGGG ACCCGAAAGA UGGUGAACUA UGCCUGAAUA GGGUGAAGCC AGAGGAAACU CUGGUGGAGG CUCGUAGCGG UUCUGACGUG CAAAUCGAUC GUCGAAUUUG GGUAUAGGGG CGAAAGACUA AUCGAACCAU CUAGUAGCUG GUUCCUGCCG AAGUUUCCCU CAGGAUAGCA GAAGCUCGUA UCAGUUUUAU GAGGUAAAGC GAAUGAUUAG AGGUUCCGGG GUCGAAAUGA CCUUGACCUA UUCUCAAACU UUAAAUAUGU AAGAAGUCCU UGUUACUUAA UUGAACGUGG ACAUUUGAAU GAAGAGCUUU UAGUGGGCCA UUUUUGGUAA GCAGAACUGG CGAUGCGGGA UGAACCGAAC GUAGAGUUAA GGUGCCGGAA UACACGCUCA UCAGACACCA CAAAAGGUGU UAGUUCAUCU AGACAGCCGG ACGGUGGCCA UGGAAGUCGG AAUCCGCUAA GGAGUGUGUA ACAACUCACC GGCCGAAUGA ACUAGCCCUG AAAAUGGAUG GCGCUCAAGC GUGUUACCUA UACUCUACCG UCAGGGUUGA UAUGAUGCCC UGACGAGUAG GCAGGCGUGG AGGUCAGUGA CGAAGCCUAG ACCGUAAGGU CGGGUCGAAC GGCCUCUAGU GCAGAUCUUG GUGGUAGUAG CAAAUAUUCA AAUGAGAACU UUGAAGACUG AAGUGGGGAA AGGUUCCACG UCAACAGCAG UUGGACGUGG GUUAGUCGAU CCUAAGAGAU GGGGAAGCUC CGUUUCAAAG GCCUGAUUUU AUGCAGGCCA CCAUCGAAAG GGAAUCCGGU UAAGAUUCCG GAACCUGGAU AUGGAUUCUU CACGGUAACG UAACUGAAUG UGGAGACGUC GGCGCGAGCC CUGGGAGGAG UUAUCUUUUC UUCUUAACAG CUUAUCACCC CGGAAUUGGU UUAUCCGGAG AUGGGGUCUU AUGGCUGGAA GAGGCCAGCA CCUUUGCUGG CUCCGGUGCG CUUGUGACGG CCCGUGAAAA UCCACAGGAA GGAAUAGUUU UCAUGCCAGG UCGUACUGAU AACCGCAGCA GGUCUCCAAG GUGAACAGCC UCUAGUUGAU AGAAUAAUGU AGAUAAGGGA AGUCGGCAAA AUAGAUCCGU AACUUCGGGA UAAGGAUUGG CUCUAAGGGU CGGGUAGUGA GGGCCUUGGU CAGACGCAGC GGGCGUGCUU GUGGACUGCU UGGUGGGGCU UGCUCUGCUA GGCGGACUAC UUGCGUGCCU UGUUGUAGAC GGCCUUGGUA GGUCUCUUGU AGACCGUCGC UUGCUACAAU UAACGAUCAA CUUAGAACUG GUACGGACAA GGGGAAUCUG ACUGUCUAAU UAAAACAUAG CAUUGCGAUG GUCAGAAAGU GAUGUUGACG CAAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAAC(PSU)A(PSU) GAC(PSU)C(PSU)CUUA AGGUAGCCAA AUGCCUCGUC AUCUAAUUAG UGACGCGCAU GAAUGGAUUA ACGAGAUUCC CACUGUCCCU AUCUACUAUC UAGCGAAACC ACAGCCAAGG GAACGGGCUU GGCAGAAUCA GCGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUACC ACUACCUUUA UAGUUUCUUU ACUUAUUCAA UGAAGCGGAG CUGGAAUUCA UUUUCCACGU UCUAGCAUUC AAGGUCCCAU UCGGGGCUGA UCCGGGUUGA AGACAUUGUC AGGUGGGGAG UUUGGCUGGG GCGGCACAUC UGUUAAACGA UAACGCAGAU GUCCUAAGGG GGGCUCAUGG AGAACAGAAA UCUCCAGUAG AACAAAAGGG UAAAAGCCCC CUUGAUUUUG AUUUUCAGUG UGAAUACAAA CCAUGAAAGU GUGGCCUAUC GAUCCUUUAG UCCCUCGGAA UUUGAGGCUA GAGGUGCCAG AAAAGUUACC ACAGGGAUAA CUGGCUUGUG GCAGUCAAGC GUUCAUAGCG ACAUUGCUUU UUGAUUCUUC GAUGUCGGCU CUUCCUAUCA UACCGAAGCA GAAUUCGGUA AGCGUUGGAU UGUUCACCCA CUAAUAGGGA ACGUGAGCUG GGUUUAGACC GUCGUGAGAC AGGUUAGUUU UACCCUACUG AUGAAUGUUA CCGCAAUAGU AAUUGAACUU AGUACGAGAG GAACAGUUCA UUCGGAUAAU UGGUUUUUGC GGCUGUCUGA UCAGGCAUUG CCGCGAAGCU ACCAUCCGCU GGAUUAUGGC UGAACGCCUC UAAGUCAGAA UCCAUGCUAG AACGCGGUGA UUUCUUUGCU CCACACAAUA UAGAUGGAUA CGAAUAAGGC GUCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGGG GAUAAAUCAU UUGUAUACGA CUUAGAUGUA CAACGGGGUA UUGUAAGCAG UAGAGUAGCC UUGUUGUUAC GAUCUGCUGA GAUUAAGCCU UUGUUGUCUG AUUUGU
MassTheoretical: 1.097493875 MDa
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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Component #5: nucleic-acid, Saccharomyces cerevisiae strain HB_C_OMARUNUI_6 chr...

Nucleic-acidName: Saccharomyces cerevisiae strain HB_C_OMARUNUI_6 chromosome XII sequence
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGGU GACCAUACGC GAAACUCAGG UGCUGCAAUC U
MassTheoretical: 38.951105 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #6: nucleic-acid, Saccharomyces cerevisiae culture-collection CBS:288...

Nucleic-acidName: Saccharomyces cerevisiae culture-collection CBS:2888 large subunit ribosomal RNA gene, partial sequence
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAACUUUCAA CAACGGAUCU CUUGGUUCUC GCAUCGAUGA AGAACGCAGC GAAAUGCGAU ACGUAAUGUG AAUUGCAGAA UUCCGUGAAU CAUCGAAUCU UUGAACGCAC AUUGCGCCCC UUGGUAUUCC AGGGGGCAUG CCUGUUUGAG CGUCAUUU
MassTheoretical: 50.682922 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #7: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-A / Recombinant expression: No
MassTheoretical: 27.463574 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #8: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Recombinant expression: No
MassTheoretical: 43.850793 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #9: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-A / Recombinant expression: No
MassTheoretical: 39.159125 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #10: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 33.764828 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #11: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-A / Recombinant expression: No
MassTheoretical: 20.000564 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #12: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-A / Recombinant expression: No
MassTheoretical: 27.686281 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #13: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-A / Recombinant expression: No
MassTheoretical: 28.17582 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #14: protein, 60S ribosomal protein L9-A

ProteinName: 60S ribosomal protein L9-A / Recombinant expression: No
MassTheoretical: 21.605061 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #15: protein, 60S ribosomal protein L10

ProteinName: 60S ribosomal protein L10 / Recombinant expression: No
MassTheoretical: 25.410465 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #16: protein, 60S ribosomal protein L11-A

ProteinName: 60S ribosomal protein L11-A / Recombinant expression: No
MassTheoretical: 19.755691 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #17: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-A / Recombinant expression: No
MassTheoretical: 22.604164 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #18: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-A / Recombinant expression: No
MassTheoretical: 15.195066 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #19: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-A / Recombinant expression: No
MassTheoretical: 24.482357 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #20: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-A / Recombinant expression: No
MassTheoretical: 22.247227 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #21: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-A / Recombinant expression: No
MassTheoretical: 20.589518 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #22: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-A / Recombinant expression: No
MassTheoretical: 20.609252 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #23: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-A / Recombinant expression: No
MassTheoretical: 21.762316 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #24: protein, 60S ribosomal protein L20-A

ProteinName: 60S ribosomal protein L20-A / Recombinant expression: No
MassTheoretical: 20.478852 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #25: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-A / Recombinant expression: No
MassTheoretical: 18.279266 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #26: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-A / Recombinant expression: No
MassTheoretical: 13.711359 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #27: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-A / Recombinant expression: No
MassTheoretical: 14.49395 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #28: protein, 60S ribosomal protein L24-A

ProteinName: 60S ribosomal protein L24-A / Recombinant expression: No
MassTheoretical: 17.661717 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #29: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Recombinant expression: No
MassTheoretical: 15.787612 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #30: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-A / Recombinant expression: No
MassTheoretical: 14.265784 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #31: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-A / Recombinant expression: No
MassTheoretical: 15.56836 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #32: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Recombinant expression: No
MassTheoretical: 16.761666 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #33: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 6.691884 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #34: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Recombinant expression: No
MassTheoretical: 11.430364 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #35: protein, 60S ribosomal protein L31-A

ProteinName: 60S ribosomal protein L31-A / Recombinant expression: No
MassTheoretical: 12.980158 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #36: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Recombinant expression: No
MassTheoretical: 14.809441 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #37: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-A / Recombinant expression: No
MassTheoretical: 12.17713 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #38: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-A / Recombinant expression: No
MassTheoretical: 13.673196 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #39: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-A / Recombinant expression: No
MassTheoretical: 13.94264 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #40: protein, 60S ribosomal protein L36-A

ProteinName: 60S ribosomal protein L36-A / Recombinant expression: No
MassTheoretical: 11.151259 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #41: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-A / Recombinant expression: No
MassTheoretical: 9.877395 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #42: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Recombinant expression: No
MassTheoretical: 8.845561 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #43: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Recombinant expression: No
MassTheoretical: 6.35864 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #44: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Recombinant expression: No
MassTheoretical: 14.583077 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #45: protein, 60S ribosomal protein L42-A

ProteinName: 60S ribosomal protein L42-A / Recombinant expression: No
MassTheoretical: 12.246658 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #46: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-A / Recombinant expression: No
MassTheoretical: 10.112952 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #47: protein, Ribosomal Protein uL1

ProteinName: Ribosomal Protein uL1 / Recombinant expression: No
MassTheoretical: 18.485723 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #48: protein, 60S ribosomal export protein NMD3

ProteinName: 60S ribosomal export protein NMD3 / Recombinant expression: No
MassTheoretical: 59.995926 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #49: protein, Large subunit GTPase 1

ProteinName: Large subunit GTPase 1 / Recombinant expression: No
MassTheoretical: 71.945875 kDa
SourceSpecies: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #50: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 160 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #51: ligand, POTASSIUM ION

LigandName: POTASSIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 3.909805 MDa

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Component #52: ligand, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.522196 kDa

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Component #53: ligand, water

LigandName: water / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
Support film10W
Vitrification #1Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Vitrification #2Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging #1

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 27000 X (nominal), 31000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4000 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Electron microscopy imaging #2

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: 59.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 226516
3D reconstruction #1Software: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
3D reconstruction #2Software: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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About Yorodumi

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News

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

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