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- PDB-6fyy: Structure of a partial yeast 48S preinitiation complex with eIF5 ... -

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Entry
Database: PDB / ID: 6fyy
TitleStructure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2)
Components
  • (40S ribosomal protein ...) x 17
  • (Eukaryotic translation initiation factor ...) x 9
  • 18S ribosomal RNA
  • 60S ribosomal protein L41-ARibosome
  • KLLA0A07194p
  • KLLA0A10483p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0B06182p
  • KLLA0B08173p
  • KLLA0B11231p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0E12277p
  • KLLA0E23673p
  • KLLA0F07843p
  • KLLA0F09812p
  • KLLA0F18040p
  • KLLA0F25542p
  • Ubiquitin-40S ribosomal protein S27a
  • eIF3c,Eukaryotic translation initiation factor 3 subunit C
  • mRNA (31-MER)
  • tRNAi
KeywordsRIBOSOME / ribosome / translation / initiation factors / 40S / eIF1A / eIF3 / eIF2 / eIF5 / tRNAi / 48S PIC / small ribosome subunit
Function / homologyTranslation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 3 subunit I / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Eukaryotic translation initiation factor 3 subunit C / eIF3B, RNA recognition motif ...Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 3 subunit I / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Eukaryotic translation initiation factor 3 subunit C / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / eIF3G, RNA recognition motif / RNA-binding domain superfamily / Translation initiation factor 2, alpha subunit, middle domain superfamily / RNA-binding S4 domain superfamily / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S19e domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S11 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Eukaryotic translation initiation factor 3 subunit G, N-terminal / Ribosomal protein S7 domain / Elongation factor Tu GTP binding domain / Translation initiation factor 1A (eIF-1A), conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S3, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Eukaryotic translation initiation factor 3 subunit G / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5, N-terminal / Ribosomal protein S21e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S19, superfamily / Ribosomal protein S15P / RNA-binding domain, S1 / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S19 conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin / Ubiquitin conserved site / WD40 repeat, conserved site / Ribosomal protein S8e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Ribosomal protein S17e signature. / Eukaryotic translation initiation factor 2 alpha subunit / Eukaryotic translation initiation factor 3 subunit G / Initiation factor eIF2 gamma, C terminal / Eukaryotic translation initiation factor eIF2A / RS4NT (NUC023) domain / Ribosomal S13/S15 N-terminal domain / KH domain / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Ribosomal_S17 N-terminal / Ribosomal protein L41 / Ribosomal protein S30 / Ribosomal protein S5, C-terminal domain / Plectin/S10 domain / S25 ribosomal protein / Elongation factor Tu domain 2 / 40S ribosomal protein S4 C-terminus / Ribosomal protein S7 signature. / Domain found in IF2B/IF5 / Ribosomal protein S24e signature. / Ribosomal protein S13 signature. / Ribosomal protein S4 signature. / Ribosomal protein S19e signature. / Ribosomal protein S5 signature. / Ribosomal protein S6e signature. / Ribosomal protein S3 signature.
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.02 Å resolution
AuthorsLlacer, J.L. / Hussain, T. / Gordiyenko, Y. / Ramakrishnan, V.
CitationJournal: Elife / Year: 2018
Title: Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.
Authors: José Luis Llácer / Tanweer Hussain / Adesh K Saini / Jagpreet Singh Nanda / Sukhvir Kaur / Yuliya Gordiyenko / Rakesh Kumar / Alan G Hinnebusch / Jon R Lorsch / V Ramakrishnan
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 12, 2018 / Release: Dec 5, 2018

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Structure visualization

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Assembly

Deposited unit
1: tRNAi
2: 18S ribosomal RNA
3: mRNA (31-MER)
A: 40S ribosomal protein S0
B: 40S ribosomal protein S1
C: KLLA0F09812p
D: KLLA0D08305p
E: 40S ribosomal protein S4
F: KLLA0D10659p
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: KLLA0E23673p
K: KLLA0B08173p
L: KLLA0A10483p
M: 40S ribosomal protein S12
N: KLLA0F18040p
O: 40S ribosomal protein S14
P: KLLA0F07843p
Q: 40S ribosomal protein S16
R: KLLA0B01474p
S: KLLA0B01562p
T: KLLA0A07194p
U: KLLA0F25542p
V: 40S ribosomal protein S21
W: 40S ribosomal protein S22
X: KLLA0B11231p
Y: 40S ribosomal protein S24
Z: KLLA0B06182p
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
f: Ubiquitin-40S ribosomal protein S27a
g: KLLA0E12277p
h: 60S ribosomal protein L41-A
i: Eukaryotic translation initiation factor 1A
j: Eukaryotic translation initiation factor 2 subunit alpha
k: Eukaryotic translation initiation factor 2 subunit gamma
l: Eukaryotic translation initiation factor 2 subunit beta
m: Eukaryotic translation initiation factor 5
o: Eukaryotic translation initiation factor 3 subunit A
p: Eukaryotic translation initiation factor 3 subunit B
q: eIF3c,Eukaryotic translation initiation factor 3 subunit C
r: Eukaryotic translation initiation factor 3 subunit G
s: Eukaryotic translation initiation factor 3 subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,762,414171
Polyers1,758,57347
Non-polymers3,841124
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)276650
ΔGint (kcal/M)-2952
Surface area (Å2)528760
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain tRNAi


Mass: 24799.072 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)
#2: RNA chain 18S ribosomal RNA /


Mass: 579454.875 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: GenBank: 49642208
#3: RNA chain mRNA (31-MER)


Mass: 15344.964 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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40S ribosomal protein ... , 17 types, 17 molecules ABEGHIMOQVWYabcde

#4: Protein/peptide 40S ribosomal protein S0 /


Mass: 28264.525 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CN12
#5: Protein/peptide 40S ribosomal protein S1 /


Mass: 29013.678 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWD0
#8: Protein/peptide 40S ribosomal protein S4 /


Mass: 29617.514 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWJ2
#10: Protein/peptide 40S ribosomal protein S6 /


Mass: 26970.391 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CM04
#11: Protein/peptide 40S ribosomal protein S7 /


Mass: 21735.297 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CTD6
#12: Protein/peptide 40S ribosomal protein S8 /


Mass: 22642.727 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CMG3
#16: Protein/peptide 40S ribosomal protein S12 /


Mass: 14466.398 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CLU4
#18: Protein/peptide 40S ribosomal protein S14 / / RP59


Mass: 14530.655 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P27069
#20: Protein/peptide 40S ribosomal protein S16 /


Mass: 15874.531 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q875N2
#25: Protein/peptide 40S ribosomal protein S21 /


Mass: 9797.949 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CXT6
#26: Protein/peptide 40S ribosomal protein S22 /


Mass: 14645.041 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CW21
#28: Protein/peptide 40S ribosomal protein S24 /


Mass: 15194.549 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CU44
#30: Protein/peptide 40S ribosomal protein S26 /


Mass: 13539.957 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CS01
#31: Protein/peptide 40S ribosomal protein S27 /


Mass: 8884.362 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CNL2
#32: Protein/peptide 40S ribosomal protein S28 / / S33


Mass: 7549.824 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P33285
#33: Protein/peptide 40S ribosomal protein S29 /


Mass: 6662.570 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CPG3
#34: Protein/peptide 40S ribosomal protein S30 /


Mass: 7141.421 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CUH5

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Protein/peptide , 18 types, 18 molecules CDFJKLNPRSTUXZfghq

#6: Protein/peptide KLLA0F09812p


Mass: 27649.979 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CKL3
#7: Protein/peptide KLLA0D08305p


Mass: 26300.535 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CRK7
#9: Protein/peptide KLLA0D10659p


Mass: 25385.975 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CRA3
#13: Protein/peptide KLLA0E23673p


Mass: 21587.049 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CM18
#14: Protein/peptide KLLA0B08173p


Mass: 12584.377 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CVZ5
#15: Protein/peptide KLLA0A10483p


Mass: 17843.930 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CX80
#17: Protein/peptide KLLA0F18040p


Mass: 16989.875 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CJK0
#19: Protein/peptide KLLA0F07843p


Mass: 15986.796 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CKV4
#21: Protein/peptide KLLA0B01474p


Mass: 15722.216 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWU3
#22: Protein/peptide KLLA0B01562p


Mass: 17084.602 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CWT9
#23: Protein/peptide KLLA0A07194p


Mass: 15879.010 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CXM0
#24: Protein/peptide KLLA0F25542p


Mass: 13337.604 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CIM1
#27: Protein/peptide KLLA0B11231p


Mass: 16047.897 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: F2Z602
#29: Protein/peptide KLLA0B06182p


Mass: 12002.116 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CW78
#35: Protein/peptide Ubiquitin-40S ribosomal protein S27a


Mass: 17110.977 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P69061
#36: Protein/peptide KLLA0E12277p


Mass: 35830.945 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: Q6CNI7
#37: Protein/peptide 60S ribosomal protein L41-A / Ribosome / L47 / Large ribosomal subunit protein eL41-A / YL41


Mass: 3354.243 Da / Num. of mol.: 1
Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
References: UniProt: P0CX86
#45: Protein/peptide eIF3c,Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 93 kDa subunit / eIF3 p93 / Nuclear transport protein NIP1 / Translation initiation factor eIF3 / p93 subunit


Mass: 86539.539 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: NIP1, YMR309C, YM9924.01C, YM9952.11C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32497

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Eukaryotic translation initiation factor ... , 9 types, 9 molecules ijklmoprs

#38: Protein/peptide Eukaryotic translation initiation factor 1A / eIF-1A / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 17462.168 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF11, YMR260C, YM8156.02C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38912
#39: Protein/peptide Eukaryotic translation initiation factor 2 subunit alpha / eIF-2-alpha


Mass: 34763.652 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P20459
#40: Protein/peptide Eukaryotic translation initiation factor 2 subunit gamma / eIF-2-gamma


Mass: 57942.699 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: GCD11, TIF213, YER025W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32481
#41: Protein/peptide Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 31631.309 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: SUI3, TIF212, YPL237W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P09064
#42: Protein/peptide Eukaryotic translation initiation factor 5 / eIF-5


Mass: 45321.977 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF5, YPR041W, YP3085.05 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38431
#43: Protein/peptide Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 110 kDa subunit homolog / eIF3 p110 / Translation initiation factor eIF3 / p110 subunit homolog


Mass: 110517.641 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: RPG1, TIF32, YBR079C, YBR0734 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38249
#44: Protein/peptide Eukaryotic translation initiation factor 3 subunit B / eIF3b / Cell cycle regulation and translation initiation protein / Eukaryotic translation initiation factor 3 90 kDa subunit / eIF3 p90 / Translation initiation factor eIF3 p90 subunit


Mass: 88241.766 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: PRT1, CDC63, YOR361C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P06103
#46: Protein/peptide Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Translation initiation factor eIF3 p33 subunit homolog / eIF3 p33 homolog


Mass: 30520.502 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF35, SCY_1313 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZZ25
#47: Protein/peptide Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 39 kDa subunit homolog / eIF-3 39 kDa subunit homolog


Mass: 38803.375 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: TIF34, SCY_4321 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: A6ZMK5

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Non-polymers , 4 types, 124 molecules

#48: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 117 / Formula: Mg / Magnesium
#49: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Formula: Zn / Zinc
#50: Chemical ChemComp-MET / METHIONINE


Mass: 149.211 Da / Num. of mol.: 1 / Formula: C5H11NO2S / Methionine
#51: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Formula: C11H18N5O13P3 / Comment: GMP-PCP (energy-carrying molecule analogue) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C2)RIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,470MULTIPLE SOURCES
2RibosomeRIBOSOME2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,371NATURAL
3tRNACOMPLEX11NATURAL
4initiation factorsCOMPLEX39,40,41,43,44,45,46,471RECOMBINANT
5initiation factorsCOMPLEX38,421RECOMBINANT
6mRNACOMPLEX31RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12284590Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
234932Saccharomyces cerevisiae (baker's yeast)
344932Saccharomyces cerevisiae (baker's yeast)
454932Saccharomyces cerevisiae (baker's yeast)
564932Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
144932Saccharomyces cerevisiae (baker's yeast)
25469008Escherichia coli BL21(DE3) (bacteria)
3632630synthetic construct (others)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer ID
120 mMMES1
25 mMMagnessium acetate1
380 mMPotassium acetate1
410 mMAmmonium acetate1
52 mMDithiothreitol (DTT)1
60.001 mMZinc acetate1
70.6 mMATP1
80.25 mMGDPCP1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 78000 / Calibrated magnification: 104478 / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 50 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 100 kelvins / Temperature (min): 90 kelvins
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 40 e/Å2
Details: Images were collected in movie-mode at 32 frames per second
Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 2 / Number of real images: 2100

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Processing

SoftwareName: REFMAC / Version: 5.8.0166 / Classification: refinement
EM software
IDNameVersionCategory
2EMANparticle selection
3EPUimage acquisition
5GctfCTF correction
8UCSF Chimera1.1model fitting
9Coot0.8model fitting
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
15REFMAC5.8model refinement
Image processingDetails: FEI Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 394672
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 157868 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingOverall b value: 49 / Ref protocol: OTHER / Ref space: RECIPROCAL / Target criteria: FSC
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLOverall ESU RSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1120.7260.080.430.33-0.57-0.160.490.8910.288890.288893.05268.001364807100.0012.0820.2020.2920.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 104243
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.016110873
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.1941.671157654
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg17.9978.22618481
ELECTRON MICROSCOPYr_dihedral_angle_2_deg43.05023.1752709
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.25815.00011353
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.38215.000541
ELECTRON MICROSCOPYr_chiral_restr0.1170.20717870
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02167484
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.04814.22832494
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it3.69521.32540483
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.97911.02978379
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined9.059196831
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.05 Å / R factor R work: 0.576 / Lowest resolution: 3.129 Å / Number reflection R free: 0 / Number reflection R work: 100930 / Total number of bins used: 20 / Percent reflection obs: 1

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