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- EMDB-9242: Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state) -

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Basic information

Entry
Database: EMDB / ID: 9242
TitleRabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
Map dataPostprocessed map
SampleRabbit 80S ribosome with eEF2 and SERBP1 (rotated state):
(nucleic-acidNucleic acid) x 4 / uL2 / uL3 / uL4 / uL18 / eL6 / uL30 / eL8 / uL6 / uL16 ...(nucleic-acidNucleic acid) x 4 / uL2 / uL3 / uL4 / uL18 / eL6 / uL30 / eL8 / uL6 / uL16 / uL5 / eL13 / eL14 / eL15List of Subaru engines / uL13 / uL22 / eL18 / eL19 / eL20 / eL21 / eL22 / uL14 / eL24 / uL23 / uL24 / eL27 / uL15 / eL29 / eL30 / eL31 / eL32CD59 / eL33 / eL34 / uL29 / eL36 / eL37 / eL38 / eL39 / eL40 / eL41 / eL42 / eL43 / eL28 / uL10 / uL11 / eEF2 / SERBP1 / uS2 / eS1 / uS5 / uS3 / eS4 / uS7 / eS6 / eS7 / eS8 / uS4 / eS10 / uS17 / eS12 / uS15 / uS11 / uS19 / uS9 / eS17 / uS13 / eS19 / uS10 / eS21 / uS8 / uS12 / eS24 / eS25 / eS26 / eS27 / eS28 / uS14 / eS30 / eS31 / RACK1Receptor for activated C kinase 1 / (ligand) x 3
Function / homologyRibosomal protein L30e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site ...Ribosomal protein L30e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L31e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S3, conserved site / Ribosomal protein L19/L19e conserved site / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L2, archaeal-type / Ribosomal protein L39e domain superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L31e domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S15P / Ribosomal L37ae protein family / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S21e, conserved site / 50S ribosomal protein L30e-like / Zinc-binding ribosomal protein / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / Ribosomal protein L25/L23 / Ribosomal protein L30, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Ribosomal protein L37ae/L37e / Ribosomal protein L2, domain 2 / TRASH domain / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Translation protein, beta-barrel domain superfamily / Translation protein SH3-like domain superfamily / Ribosomal protein L34Ae / Ribosomal protein S30 / Ribosomal protein S12/S23 / Ribosomal protein L7, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 3 / Ribosomal protein S17e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L30, conserved site / WD40-repeat-containing domain
Function and homology information
SourceOryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsBrown A / Baird MR / Yip MCJ / Murray J / Shao S
CitationJournal: Elife / Year: 2018
Title: Structures of translationally inactive mammalian ribosomes.
Authors: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao
Abstract: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.
Validation ReportPDB-ID: 6mte

SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mte
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9242.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. Å
400 pix
1.34 Å/pix.
= 536. 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:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.385669 - 0.67855746
Average (Standard dev.)0.0017560415 (0.022576272)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3860.6790.002

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Supplemental data

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Sample components

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Entire Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)

EntireName: Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
Number of components: 87

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Component #1: protein, Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)

ProteinName: Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #2: nucleic-acid, 28S rRNA

Nucleic-acidName: 28S rRNA28S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAA AAGAAACUAA CCAGGAUUCC CUCAGUAACG GCGAGUGAAC AGGGAAGAGC CCAGCGCCGA AUCCCCGCCC CGCGGCGGGG CGCGGGAAAU GUGGCGUACG GAAGACCCAC UCCCCGGCGC CGGGGGGCCC AAGUCCUUCU GAUCGAGGCC CAGCCCGUGG ACGGUGUGAG (B9B)CCGGUAGCG GCCCCCGGCG CGCCGGGCCC GGGUCUUCCC GGAGUCGGGU UGCUUGGGAA UGCAGCCCAA AGCGGGUGGU AAACUCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAA(OMG)GGA AAGUUGAAAA GAACUUUGAA G(A2M)GAGAGUUC AAGAGGGCGU GAAACCGUUA AGAGGUAAAC GGGUGGGGUC CGCGCAGUCC GCCCGGAGGA UUCAACCCGG CGGCGCGGUC CGGCCGUGCC GGCGGGGCGG AUCUCCCGCU CCCGUCGGCG GGGGACCGCC CCCCGGCCGG CGACCGGCCG CCGCCGGGCG CAUUUCCACC GCGGCGGUGC GCCGCGACCG GCUCCGGGAC GGCU(2MG)GGAAG GCCCCGGCGG GGAAGGUGGC CCGGGGGCCC CGGGUGUUAC AGCCCCGCCC CGGCAGCAGC AGCUCGCCGA AUCCCGGGGC CGAGGGAGCG AGACCCGUGC CGCCGCGCUC UCCCCCCUGG GGGGGCCGGG CCACCCCUCC CACGGCGCGA CCGCUGGGGC GGACUGUCCA GUGCGCCCCG GGCGGGUCGC GCCGUCGGGC CCGGGGGGCC ACGCGUCCCC CGCGAGCGCA CGGGGUCGGC GGCGAUGUCG GCUACCCACC CGACCC(OMG)UCU UG(1MA)AAC(A2M)CGG ACCAAGGAGU CUAACACG(P4U)G CGCGAGUCGG GGGCUACGAA AGCCGCCGUG GCGCAAUGAA GGUGAAGGCC GGCGGCGCGC CGCCGGCCGA GGUGGGAUCC CGAGGCCUUC CAGUCCGCCG AGGG(B8Q)GCACC ACCGGCCCGU CUCGCCCGCC GCGCCGGGGA GGUGGAGCAC GAGCGCACGU GUUAG(2MG)ACCC (OMG)A(A2M)AGAUGGU GA(A2M)CUAUGCC UGGGCAGGGC GAAGCCAGAG GAAACUCUGG UG(B9B)AGGUCCG (PSU)AGCGGUCCU GACGUGCGAA UCG(7MG)UCGUCC GACCUGGGUA UAG(OMG)GGCGAA AGACUAAUCG AACCAUCUAG UAGCUGG(I4U)UC CCUCCAAAGU UUCCC(PSU)CAGG A(PSU)AGCUGGCG CUCUCCGCAG UUUUAUCCGG UAAAGCGAAU GAUUAGAGGU CUUGGGGCCG AAACGAUCUC AACCUAUUCU CAAACUUUAA AU(E7G)GGUAAGA AGCCCGGCUC GCUGGUGUGG AGCCGGGCGU GGAAUGCGAG UGCCUAGUGG GCCAC(B8H)UUUG G(UR3)AAGC(A2M)GAA CUGGCGCU(OMG)C GGGAUGAACC GAACGCCGGG UUAA(P7G)GCGCC CGAUGCCGAC GCUCAUCAGA CCCCAGAAAA GGUGUUGGUU GAUAUAGACA GCAGGAUGGU GGCCAUGGAA GUCGGAAUCC GCUAAGGAGU GUGUAACAAC UCACCUGCCG AAUCAACUAG CCCUGAAAAU GGAUG(OMG)CGCU GGAGCGUCGG GCCCAUACCC GGCCGUCGCU GGCAGUCGGC AGAGCGAGAA AGAGAGUGGC GCGGACGCUA CGCCGCGACG AGUAGGAGGG CCGCUGCG(E7G)U GAGCCUUGAA GCCUAGGGCG CGGGCCCGGG UGGAGCCGCC GCAGGUGCAG AUCUUGGUGG UAGU(A2M)(OMG)(OMC)AAA UAUUCAAACG A(B8W)AACUUUGA AGGCCGAAGU GG(A2M)GAAGGGU UCCAUGUGAA CAG(OMC)A(OMG)UUGA ACAUGGGUCA GUCGGUCCUG AGAGAUGGGC GAGCGCCGUU CCGAAGGGAC GGGCGAUGGC CUCCGUUGCC CUCAGCCGA(PSU) CGAAAGGGAG UCG(7MG)GUUCAG AUCCCCGAAU CCGGAGUGGC GGAGAUGGGC GCCGCGAGGC GUCCAGUGCG GUAACGCGAC CGAUCCCGGA GAAGCCGGCG GGAGCCCCGG GGAGAGUUCU CUUUUCUUUG UGAAGGGCAG GGCGCCCUGG AAUGGGUUCG CCCCGAGAGA GGGGCCCGUG CCUUGGAAAG CGUCGCGGUU CCGGCGGCGU CCGGUGAGCU CUCGCUGGCC CUUGAAAAUC CGGGG(B9B)AGAG GGUGUAAAUC UCGC(OMG)CCGGG CCGUACC(B9H)AU AUCCGCAGCA GGUCU(OMC)CAAG GUGAACAGCC UCUGGCAUGU UGGAACAAUG UAGGUAAGGG AAGUCGGCAA GC(OMC)GGAUCCG UAACUUCGGG AUAAGGAUUG GCUCUAAGGG CUGGCAGCCG ACUUAGAACU GGUGCGGACC AGGGGAAUCC GACUGUUUAA UUAAAACAAA GCAUCGCGAA GGCCCGCGGC GGGUGUUGAC GCGAUGUGAU UUCUGCC(OMC)AG UGCUCUGAAU G(PSU)CA(A2M)AGUG(A2M) AGAAA(PSU)UCAA UGAAGCGCGG GUAAACGGCG GGAGUAAC(B8H)A (PSU)GACUCUCUU AAGGUAGC(5MC)A A(A2M)UGCCUC(OMG)U CAUCUAAUUA GUGACGCGCA UGAAUGGAUG A(A2M)CGAGAUUC CCACUGUCCC UACCUACUAU CCAGCGAAAC CAC(A2M)G(OMC)CAAG GGAACG(P7G)GCU UGG(OMC)GGAAUC AGC(B8K)G(BGH)GAAA GAAGA(OMC)CCUG UUGAGCUUGA CUCUAGUCUG GCACGGUGAA GAGACAUGAG AAGUGUAGAA UAAGUGGGAG GCCGCCGGUG AAAUACCACU ACUCUGAUCG UUUUUUCACU GACCCGG(5MU)GA GGCGGGGGGG CGAGCCGGGC UCUCGCUUCU GGCGCCAA(B8W)C GCCCGGCCGG CCGGGCGCGA CCCGCUCCGG GGACAGUGCC AGGUGGG(B8W)AG UUUGAC(I4U)G(OMG)G GCGGUACACC UGUCAAACGG UA(6MZ)CGCAGGU GUCCUAAGGC GAGCUCAGGG AGGACAGAAA CCUCCCGUGG AGCAGAAGGG CAAAAGCUCG CUUGA(PSU)CU(B8H)G AUUUUCAG(OMU)A CGAAUACAGA CCGUGAAAGC GGGGCCU(5MC)AC GAUCCUUCUG ACCUUUU(E6G)GG UUUUAAGCAG GA(OMG)(MHG)UGUCAG AAAAGUUACC ACAGGGAUAA CUGGC(PSU)UGUG GCGGCCA(1MA)GC GUUCAUAGCG ACGUCGCUUU UUGA(PSU)CCUU(5MC) GA(PSU)GUCGGCU CUUCCUAUCA UUGU(B8W)AAGCA GAAUU(B8T)ACCA AGCGUU(OMG)GAU UG(PSU)UCACCCA CUAAUAGGGA ACGUG(A2M)GCUG G(B8W)(UR3)(PSU)UAGA(OMC)C GUCGUGAGAC AG(7MG)UUAGUUU UACCCU(M7A)CUG AUG(A2M)UGUGUU GUUGCCAUGG UAAUCCUGC(UR3) CAGUACGAGA GGAACCGCAG GU(OMU)CA(OMG)ACAU (PSU)UGGUGUA(PSU)(OMG) UGCUUGGCUG AGGAGCCAAU GGGGCGAAGC UAC(B8T)AUCUGU GGGAUUAUGA CU(B8K)AACGCCU CUAAGUCAGA AUCCCGCCCA GGCGGAACGA UAGCGCCGGA GCCUCGGUUG GCCUCGGAUA GCCGGUCCCC CGCCGGGGUC CGGU(OMG)C(2MG)GAG AGCCCUUCGU CCCGGGAAAC GGGGCGGCCG GAAAGGGGGC CGCCCUCUCG CCCGUCACGC ACCGCACGUU CGUGGGGAAC CUGGCGCUAA ACCAUUCGUA GACGACCUGC UUCUGGGUCG GGGUUUCGUA CGUAGCAGAG CAGCUGCUGC GAUCUAUUGA AAGUCAGCCC UCGACACAAG GGUUUGU
MassTheoretical: 1.167366125 MDa
SourceSpecies: Rabbit (rabbit)

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Component #3: nucleic-acid, 5S rRNA

Nucleic-acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCUACGGCC AUACCACCCU GAACGCGCCC GAUCUCGUCU GAUCUCGGAA GCUAAGCAGG GUCGGGCCUG GUUAGUACUU GGAUGGGAGA CCGCCUGGGA AUACCGGGUG CUGUAGGCUU
MassTheoretical: 38.691914 kDa
SourceSpecies: Rabbit (rabbit)

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Component #4: nucleic-acid, 5.8S rRNA

Nucleic-acidName: 5.8S rRNA5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGACUCUUAG CGG(OMU)GGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGU UGAUCAUCGA CACUUCGAAC GCACUUGCGG CCCCGGGUUC CUCCCGGGGC UACGCCUGUC UGAGCGUCGC U
MassTheoretical: 48.559699 kDa
SourceSpecies: Rabbit (rabbit)

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Component #5: protein, uL2

ProteinName: uL2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.998613 kDa
SourceSpecies: Rabbit (rabbit)

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Component #6: protein, uL3

ProteinName: uL3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.119812 kDa
SourceSpecies: Rabbit (rabbit)

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Component #7: protein, uL4

ProteinName: uL4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.114434 kDa
SourceSpecies: Rabbit (rabbit)

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Component #8: protein, uL18

ProteinName: uL18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.077391 kDa
SourceSpecies: Rabbit (rabbit)

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Component #9: protein, eL6

ProteinName: eL6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.028336 kDa
SourceSpecies: Rabbit (rabbit)

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Component #10: protein, uL30

ProteinName: uL30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.658754 kDa
SourceSpecies: Rabbit (rabbit)

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Component #11: protein, eL8

ProteinName: eL8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.221516 kDa
SourceSpecies: Rabbit (rabbit)

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Component #12: protein, uL6

ProteinName: uL6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.627215 kDa
SourceSpecies: Rabbit (rabbit)

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Component #13: protein, uL16

ProteinName: uL16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.643057 kDa
SourceSpecies: Rabbit (rabbit)

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Component #14: protein, uL5

ProteinName: uL5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.399498 kDa
SourceSpecies: Rabbit (rabbit)

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Component #15: protein, eL13

ProteinName: eL13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.200525 kDa
SourceSpecies: Rabbit (rabbit)

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Component #16: protein, eL14

ProteinName: eL14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.217355 kDa
SourceSpecies: Rabbit (rabbit)

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Component #17: protein, eL15

ProteinName: eL15List of Subaru engines / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.076088 kDa
SourceSpecies: Rabbit (rabbit)

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Component #18: protein, uL13

ProteinName: uL13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.144859 kDa
SourceSpecies: Rabbit (rabbit)

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Component #19: protein, uL22

ProteinName: uL22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.758678 kDa
SourceSpecies: Rabbit (rabbit)

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Component #20: protein, eL18

ProteinName: eL18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.568492 kDa
SourceSpecies: Rabbit (rabbit)

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Component #21: protein, eL19

ProteinName: eL19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.613033 kDa
SourceSpecies: Bovine (cattle)

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Component #22: protein, eL20

ProteinName: eL20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.827561 kDa
SourceSpecies: Rabbit (rabbit)

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Component #23: protein, eL21

ProteinName: eL21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.478791 kDa
SourceSpecies: Rabbit (rabbit)

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Component #24: protein, eL22

ProteinName: eL22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.495275 kDa
SourceSpecies: Rabbit (rabbit)

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Component #25: protein, uL14

ProteinName: uL14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.972425 kDa
SourceSpecies: Rabbit (rabbit)

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Component #26: protein, eL24

ProteinName: eL24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.825111 kDa
SourceSpecies: Rabbit (rabbit)

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Component #27: protein, uL23

ProteinName: uL23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.727181 kDa
SourceSpecies: Rabbit (rabbit)

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Component #28: protein, uL24

ProteinName: uL24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.891787 kDa
SourceSpecies: Rabbit (rabbit)

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Component #29: protein, eL27

ProteinName: eL27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.704635 kDa
SourceSpecies: Rabbit (rabbit)

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Component #30: protein, uL15

ProteinName: uL15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.489363 kDa
SourceSpecies: Rabbit (rabbit)

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Component #31: protein, eL29

ProteinName: eL29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.708707 kDa
SourceSpecies: Rabbit (rabbit)

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Component #32: protein, eL30

ProteinName: eL30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.914756 kDa
SourceSpecies: Rabbit (rabbit)

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Component #33: protein, eL31

ProteinName: eL31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.635694 kDa
SourceSpecies: Rabbit (rabbit)

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Component #34: protein, eL32

ProteinName: eL32CD59 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.022021 kDa
SourceSpecies: Rabbit (rabbit)

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Component #35: protein, eL33

ProteinName: eL33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.449612 kDa
SourceSpecies: Rabbit (rabbit)

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Component #36: protein, eL34

ProteinName: eL34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.994621 kDa
SourceSpecies: Rabbit (rabbit)

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Component #37: protein, uL29

ProteinName: uL29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.435403 kDa
SourceSpecies: Rabbit (rabbit)

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Component #38: protein, eL36

ProteinName: eL36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.888371 kDa
SourceSpecies: Rabbit (rabbit)

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Component #39: protein, eL37

ProteinName: eL37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.090891 kDa
SourceSpecies: Rabbit (rabbit)

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Component #40: protein, eL38

ProteinName: eL38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.107752 kDa
SourceSpecies: Rabbit (rabbit)

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Component #41: protein, eL39

ProteinName: eL39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.324579 kDa
SourceSpecies: Rabbit (rabbit)

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Component #42: protein, eL40

ProteinName: eL40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.212593 kDa
SourceSpecies: Rabbit (rabbit)

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Component #43: protein, eL41

ProteinName: eL41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.473451 kDa
SourceSpecies: Rabbit (rabbit)

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Component #44: protein, eL42

ProteinName: eL42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.070474 kDa
SourceSpecies: Rabbit (rabbit)

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Component #45: protein, eL43

ProteinName: eL43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.168153 kDa
SourceSpecies: Rabbit (rabbit)

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Component #46: protein, eL28

ProteinName: eL28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.220686 kDa
SourceSpecies: Rabbit (rabbit)

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Component #47: protein, uL10

ProteinName: uL10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.521062 kDa
SourceSpecies: Rabbit (rabbit)

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Component #48: protein, uL11

ProteinName: uL11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.561117 kDa
SourceSpecies: Rabbit (rabbit)

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Component #49: protein, eEF2

ProteinName: eEF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.587258 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #50: protein, SERBP1

ProteinName: SERBP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.25769 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #51: nucleic-acid, 18S rRNA

Nucleic-acidName: 18S rRNA18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAU(A2M)UGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGU(OMU)CC(PSU)U (OMU)GGUCGCUCG UACUUGGAUA ACUGUGGUA(A2M) UUCUAG(A2M)GCU AAUA(OMC)AUGCC GACGGGCGCU GACCCCCUUC GCGGGGGGGA UGCGUGCAUU UAUCAGUGGU GACUCUAGAU AACCUCGGGC CGAUCGCACG CCCGGCGGCG ACGACCCAUU CGAACGUCUG CCCUAUCAAC UUUCGAUGGU AGUCGCCGUG CCUACCAUGG UGACCACGGG UGACGGGGAA UCAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAACGGCUA CCACAUCCAA GGAAGGCAGC AGGCGCGC(A2M)A AUUACCCACU CCCGACCCGG GGA(OMG)GUAGUG A(OMC)GAAAAAUA ACAAUACAGG ACUCUUUCGA GGCCCUGUAA UUGGAAUGAG UC(E3C)ACUUUAA AUCCUUUAAC GAGGAUCCAU UGGAGGGCAA GUCUGG(PSU)GCC AGCAGCCGCG GUAAUUCCAG CUCCAAUA(OMG)C GUAUAUUAAA GUUGCUGCAG UU(A2M)AAAAGCU CGUAGUU(OMG)GA UCUUGGGAGC GGCCGUCCCC UGCUCGGCGC CGGCCCGAAG CGUUUACUUU GAAAAAA(5MU)UA GAGUG(PSU)(PSU)CAA AGCAGGCCGC CUGGAUACCG CAGCUAGGAA UAAUGGAAUA GGACCGCGGU UCUAUUUUGU UGGUUUUCGG AACUGAGGCC AUGAUUAAGA GGGACGGCCG GGGGCAUUCG UAUUGCGCCG CUAGAGGUGA AAUUCUUGGA CCGGCGCAAG ACGGACCAGA GCGAAAGCAU UUGCCAAGAA UGUUUUCAUU AAUCAAGA(A2M)C GAAAGUCGGA GGUUCGAAGA CGAUCAGAUA CCGUCGUAGU UCCGACCA(PSU)A AACGAUGCCG ACUGGCGAUG CGGCGGCGUU AUUCCCAUGA CCCGCCGGGC AGCUUCCGGG AAACCAAAGU CUUUGGGUUC CGGGGGGAGU AUGGUUGCAA AGCUGAAACU UAAAGGAAUU GACGGAAGGG CACCAC(B8Q)AGG AGUGGAGCCU GCGGCUUAAU (PSU)UGAC(B8N)CAAC ACGGGAAACC UCACCCGGCC CGGACACGGA CAGGAUUGAC AGAUUGAUAG CUCUUUCUCG AUUCCGUGGG UGGUGGUGCA UGGC(4AC)GUUCU UAGUUGGUGG AGCGAUUUGU CUGGUUAAUU C(5MC)GAUAACGA ACGAGACUCU GGCAUGCUAA CUAGUUACGC GACCCCGGUC GGCGUAACUU CUUAGAGGGA CAAGUGGCGU UCAGCCACCC GAGAUUGAGC AAUAACAGGU CUGUGAUGCC CUUAGAUGUC CGGGGCUGCA CGCGCGCUAC ACUGACUGGC UCAGCGUGUG CCUACCCUAC GCCGGCAGGC GCGGGUAACC CGUUGAACCC CAUUCGUGAU GGGGAUCGGG GAUUGCAAUU AUUCCCCAUG AACGAGGAAU UCCCAGUAAG UGCGGGUCAU AAGCUUGCGU UGAUU(A2M)AGUC CCUGCCCUUU GUACACACCG (OMC)CCGUCG(OMC)UA CUACCGAUUG GAUGGUUUAG UGAGGCCCUC GGAUCGGCCC CGCCGGGGUG CCCUGGCGGA GCGCUGAGAA GACGGUCGAA CUUG(M7A)CUAUC UAGAGGAAGU AAAAGUCG(UR3)A (6MZ)CAAGGUUUC (4AC)GUAGGUG(MA6)(MA6) CCUGCGGAAG GAUCAUUA
MassTheoretical: 548.638062 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #52: protein, uS2

ProteinName: uS2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.361861 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #53: protein, eS1

ProteinName: eS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.759145 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #54: protein, uS5

ProteinName: uS5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.441846 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #55: protein, uS3

ProteinName: uS3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.215586 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #56: protein, eS4

ProteinName: eS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.523674 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #57: protein, uS7

ProteinName: uS7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.913453 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #58: protein, eS6

ProteinName: eS6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.471535 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #59: protein, eS7

ProteinName: eS7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.168914 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #60: protein, eS8

ProteinName: eS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.003012 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #61: protein, uS4

ProteinName: uS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.649633 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #62: protein, eS10

ProteinName: eS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.529682 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #63: protein, uS17

ProteinName: uS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.468826 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #64: protein, eS12

ProteinName: eS12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.048244 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #65: protein, uS15

ProteinName: uS15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.057113 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #66: protein, uS11

ProteinName: uS11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.544659 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #67: protein, uS19

ProteinName: uS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.646297 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #68: protein, uS9

ProteinName: uS9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.032804 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #69: protein, eS17

ProteinName: eS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.250714 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #70: protein, uS13

ProteinName: uS13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.898648 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #71: protein, eS19

ProteinName: eS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.611003 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #72: protein, uS10

ProteinName: uS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.395489 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #73: protein, eS21

ProteinName: eS21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.124389 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #74: protein, uS8

ProteinName: uS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.734357 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #75: protein, uS12

ProteinName: uS12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.626392 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #76: protein, eS24

ProteinName: eS24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.432125 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #77: protein, eS25

ProteinName: eS25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.526119 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #78: protein, eS26

ProteinName: eS26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.645794 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #79: protein, eS27

ProteinName: eS27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.34899 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #80: protein, eS28

ProteinName: eS28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.007069 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #81: protein, uS14

ProteinName: uS14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.559625 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #82: protein, eS30

ProteinName: eS30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.317539 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #83: protein, eS31

ProteinName: eS31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.98644 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #84: protein, RACK1

ProteinName: RACK1Receptor for activated C kinase 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.669113 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #85: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 298 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #86: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #87: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
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: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 104478.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 133480
3D reconstructionSoftware: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 5LZV
Output model

+
About Yorodumi

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Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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