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- PDB-6fec: Human cap-dependent 48S pre-initiation complex -

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Entry
Database: PDB / ID: 6fec
TitleHuman cap-dependent 48S pre-initiation complex
Components
  • (40S ribosomal protein ...) x 31
  • (EUKARYOTIC TRANSLATION INITIATION FACTOR ...) x 14
  • 18S ribosomal RNA
  • Messenger RNA (26-MER)
  • Receptor of activated protein C kinase 1
  • Transfer RNA (75-MER)
  • Ubiquitin-40S ribosomal protein S27a
KeywordsRIBOSOME / Translation initiation / 48S complex / capped mRNA / initiation factor 4B / start codon recognition
Function/homologyEukaryotic translation initiation factor 4B / eukaryotic translation initiation factor 4F complex assembly / RNA strand-exchange activity / Eukaryotic translation initiation factor 3 subunit M / Translation initiation factor 3 complex subunit L / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / RNA polymerase I-associated factor PAF67 ...Eukaryotic translation initiation factor 4B / eukaryotic translation initiation factor 4F complex assembly / RNA strand-exchange activity / Eukaryotic translation initiation factor 3 subunit M / Translation initiation factor 3 complex subunit L / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / RNA polymerase I-associated factor PAF67 / Recycling of eIF2:GDP / eIF3 subunit 6 N terminal domain / eukaryotic translation initiation factor 2 complex / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / cytoplasmic translational initiation / mammalian oogenesis stage / positive regulation of cAMP catabolic process / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of mRNA binding / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / laminin receptor activity / IRE1-RACK1-PP2A complex / signaling adaptor activity / rRNA modification in the nucleus and cytosol / negative regulation of ubiquitin protein ligase activity / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / formation of translation preinitiation complex / eukaryotic translation initiation factor 3 complex / T cell proliferation involved in immune response / Translation initiation factor 2, gamma subunit, C-terminal / TNFR1-mediated ceramide production / activation-induced cell death of T cells / 40S ribosomal protein SA C-terminus / positive regulation of DNA N-glycosylase activity / positive regulation of base-excision repair / response to TNF agonist / negative regulation of DNA repair / oxidized pyrimidine DNA binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / regulation of cell division / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of ceramide biosynthetic process / translation regulator activity / negative regulation of RNA splicing / negative regulation of endoplasmic reticulum unfolded protein response / translation factor activity, RNA binding / rescue of stalled ribosome / eukaryotic translation initiation factor 4F complex / NF-kappaB complex / 90S preribosome / ubiquitin ligase inhibitor activity / RNA strand annealing activity / negative regulation of hydrogen peroxide-induced neuron death / oxidized purine DNA binding / CSN8/PSMD8/EIF3K / Initiation factor eIF2 gamma, C terminal / protein kinase A binding / regulation of translational initiation / positive regulation of protein homooligomerization / positive regulation of endodeoxyribonuclease activity / Ribosomal scanning and start codon recognition / erythrocyte homeostasis / Peptide chain elongation / supercoiled DNA binding / negative regulation of phagocytosis / Deadenylation of mRNA / gastrulation / Proteasome component (PCI) domain / pigmentation / Selenocysteine synthesis / PCI domain profile. / ubiquitin-like protein conjugating enzyme binding / stress granule assembly / Formation of a pool of free 40S subunits / Translation initiation complex formation / regulation of establishment of cell polarity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / CSN8/PSMD8/EIF3K family / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / Eukaryotic Translation Termination / phagocytic cup / negative regulation of Wnt signaling pathway / positive regulation of mitochondrial depolarization / mTORC1-mediated signalling / nuclear-transcribed mRNA poly(A) tail shortening / Ribosomal protein S2, eukaryotic / rRNA export from nucleus / Ribosomal protein S12e signature. / Ribosomal protein S7e signature. / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal protein S3Ae signature.
Function and homology information
Specimen sourceHomo sapiens / human /
MethodElectron microscopy (6.3 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsSchaffitzel, C. / Schaffitzel, C.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structure of a human cap-dependent 48S translation pre-initiation complex.
Authors: Boris Eliseev / Lahari Yeramala / Alexander Leitner / Manikandan Karuppasamy / Etienne Raimondeau / Karine Huard / Elena Alkalaeva / Ruedi Aebersold / Christiane Schaffitzel
Abstract: Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load ...Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 31, 2017 / Release: Mar 14, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 14, 2018Structure modelrepositoryInitial release
1.1Apr 4, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
1: Eukaryotic translation initiation factor 3 subunit A
2: Eukaryotic translation initiation factor 3 subunit C
3: Eukaryotic translation initiation factor 3 subunit E
4: Eukaryotic translation initiation factor 3 subunit F
5: Eukaryotic translation initiation factor 3 subunit H
6: Eukaryotic translation initiation factor 3 subunit K
7: Eukaryotic translation initiation factor 3 subunit L
8: Eukaryotic translation initiation factor 3 subunit M
9: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D
A: 18S ribosomal RNA
F: Messenger RNA (26-MER)
G: 40S ribosomal protein S11
H: 40S ribosomal protein S16
I: 40S ribosomal protein S4, X isoform
J: 40S ribosomal protein S29
K: 40S ribosomal protein S9
L: 40S ribosomal protein S18
N: Transfer RNA (75-MER)
P: Eukaryotic translation initiation factor 2 subunit 1
Q: 40S ribosomal protein S23
R: 40S ribosomal protein S19
S: Eukaryotic translation initiation factor 2 subunit 3
U: 40S ribosomal protein S5
V: 40S ribosomal protein S30
W: 40S ribosomal protein S25
X: 40S ribosomal protein S7
Y: 40S ribosomal protein S27
Z: 40S ribosomal protein S13
a: 40S ribosomal protein S15a
b: 40S ribosomal protein S21
c: 40S ribosomal protein S2
d: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)
e: 40S ribosomal protein S17
f: 40S ribosomal protein SA
g: 40S ribosomal protein S3
h: 40S ribosomal protein S20
i: 40S ribosomal protein S3a
j: 40S ribosomal protein S14
k: 40S ribosomal protein S26
l: 40S ribosomal protein S28
m: Receptor of activated protein C kinase 1
n: 40S ribosomal protein S15
o: 40S ribosomal protein S8
p: Ubiquitin-40S ribosomal protein S27a
q: 40S ribosomal protein S6
r: 40S ribosomal protein S12
s: 40S ribosomal protein S24
t: 40S ribosomal protein S10
u: Eukaryotic translation initiation factor 4B
w: Eukaryotic translation initiation factor 3 subunit B


Theoretical massNumber of molelcules
Total (without water)2,006,44050
Polyers2,006,44050
Non-polymers00
Water7,476415
1


  • idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, h-48S pre-IC formation was confirmed by toe-printing and by cross-linking mass spectrometry.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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EUKARYOTIC TRANSLATION INITIATION FACTOR ... , 14 types, 14 molecules 123456789PSduw

#1: Protein/peptide Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


Mass: 164902.656 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens
#2: Protein/peptide Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 97923.547 Da / Num. of mol.: 1 / Mutation: A577Y / Source: (natural) Homo sapiens / Cell line: hela
#3: Protein/peptide Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 homolog / eIF-3 p48


Mass: 52281.633 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P60228
#4: Protein/peptide Eukaryotic translation initiation factor 3 subunit F / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 37846.730 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: Hela / References: EC:3.4.19.12 (ubiquitinyl hydrolase 1)
#5: Protein/peptide Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


Mass: 39952.281 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
#6: Protein/peptide Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


Mass: 25129.709 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:Q9UBQ5
#7: Protein/peptide Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 66804.766 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:Q9Y262
#8: Protein/peptide Eukaryotic translation initiation factor 3 subunit M / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


Mass: 42555.832 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:Q7L2H7
#9: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D


Mass: 42203.555 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens
#19: Protein/peptide Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 30633.297 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
#22: Protein/peptide Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 45862.441 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P41091
#32: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)


Mass: 2103.416 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens
#49: Protein/peptide Eukaryotic translation initiation factor 4B / eIF-4B


Mass: 72324.820 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / Gene: EIF4B / Plasmid name: pFastBac_eIF4B / Production host: Spodoptera frugiperda / References: UniProt:P23588
#50: Protein/peptide Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / eIF3 p110 / eIF3 p116


Mass: 124402.336 Da / Num. of mol.: 1 / Mutation: D104E, Y124F / Source: (natural) Homo sapiens / Cell line: hela

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RNA chain , 3 types, 3 molecules AFN

#10: RNA chain 18S ribosomal RNA


Mass: 572789.812 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
#11: RNA chain Messenger RNA (26-MER)


Mass: 8238.953 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / Gene: beta globin derived / Plasmid name: pET28a-MVHL-STOP2 / Production host: Escherichia coli
#18: RNA chain Transfer RNA (75-MER)


Mass: 24231.510 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: GenBank:174924

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40S ribosomal protein ... , 31 types, 31 molecules GHIJKLQRUVWXYZabcefghijklnoqrst

#12: Protein/peptide 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62280
#13: Protein/peptide 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 15975.753 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62249
#14: Protein/peptide 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29658.920 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62701
#15: Protein/peptide 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6364.426 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt:P62273
#16: Protein/peptide 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 21266.166 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P46781
#17: Protein/peptide 40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 16170.774 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62269
#20: Protein/peptide 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15757.587 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62266
#21: Protein/peptide 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 15812.286 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
#23: Protein/peptide 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 21525.941 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P46782
#24: Protein/peptide 40S ribosomal protein S30 / Small ribosomal subunit protein eS30


Mass: 6741.048 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62861
#25: Protein/peptide 40S ribosomal protein S25 / Small ribosomal subunit protein eS25


Mass: 8526.119 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62851
#26: Protein/peptide 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 21716.387 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62081
#27: Protein/peptide 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P42677
#28: Protein/peptide 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17128.191 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62277
#29: Protein/peptide 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14734.357 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt:P62244
#30: Protein/peptide 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 8896.102 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
#31: Protein/peptide 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 24814.285 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
#33: Protein/peptide 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 14578.988 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P08708
#34: Protein/peptide 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 23360.791 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt:P08865
#35: Protein/peptide 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 25158.535 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
References: UniProt:P23396, EC:4.2.99.18 (DNA-(apurinic or apyrimidinic site) lyase)
#36: Protein/peptide 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 11765.890 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P60866
#37: Protein/peptide 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 24944.408 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P61247
#38: Protein/peptide 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62263
#39: Protein/peptide 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 11315.428 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela
#40: Protein/peptide 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7263.394 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62857
#42: Protein/peptide 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 15151.948 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62841
#43: Protein/peptide 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 23902.871 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62241
#45: Protein/peptide 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 27471.535 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62753
#46: Protein/peptide 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 13766.122 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt:P25398
#47: Protein/peptide 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15188.970 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62847
#48: Protein/peptide 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P46783

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Protein/peptide , 2 types, 2 molecules mp

#41: Protein/peptide Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 34669.113 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P63244
#44: Protein/peptide Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8358.903 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / Cell line: hela / References: UniProt:P62979

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Non-polymers , 1 types, 415 molecules

#51: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Formula: H2O / : Water

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1human cap-dependent 48S translation pre-initiation complexRIBOSOME1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,500MULTIPLE SOURCES
2human cap-dependent 48S translation pre-initiation complexRIBOSOME1,2,3,4,5,6,7,8,9,10,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,501NATURAL
3mRNACOMPLEX111RECOMBINANT
4Eukaryotic translation initiation factor 4BCOMPLEX491RECOMBINANT
Molecular weightValue: 2 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens
239606Homo sapiens
349606Homo sapiens
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
13562Escherichia coli
247108Spodoptera frugiperda
Buffer solutionDetails: 20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP
pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 112000 / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2.1PARTICLE SELECTIONe2boxer.py
4CTFFIND4CTF CORRECTION
7UCSF Chimera1.10MODEL FITTING
9REFMAC5.8.0194MODEL REFINEMENT
10RELION1.4INITIAL EULER ASSIGNMENT
11RELION1.4FINAL EULER ASSIGNMENT
12RELION1.4CLASSIFICATION
13RELION1.4RECONSTRUCTION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 50604 / Algorithm: BACK PROJECTION / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1105.4580.64-0.57-1.054.34-2.56-4.980.961HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.374790.374796.30270.0095026100.00135.9670.8770.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 32425
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0180.01932657
ELECTRON MICROSCOPYr_bond_other_d0.0060.02029932
ELECTRON MICROSCOPYr_angle_refined_deg1.9151.95444216
ELECTRON MICROSCOPYr_angle_other_deg1.3763.00069307
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.5925.0003945
ELECTRON MICROSCOPYr_dihedral_angle_2_deg41.46324.4321638
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.99815.0005854
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.94215.000222
ELECTRON MICROSCOPYr_chiral_restr0.1500.2004935
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.02036132
ELECTRON MICROSCOPYr_gen_planes_other0.0050.0206629
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_it18.67439.39615825
ELECTRON MICROSCOPYr_mcbond_other18.67339.39715824
ELECTRON MICROSCOPYr_mcangle_it32.73159.03619763
ELECTRON MICROSCOPYr_mcangle_other32.73159.03619764
ELECTRON MICROSCOPYr_scbond_it19.88336.15616832
ELECTRON MICROSCOPYr_scbond_other19.88336.15616833
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other37.15455.10124454
ELECTRON MICROSCOPYr_long_range_B_refined63.43958918
ELECTRON MICROSCOPYr_long_range_B_other63.43958919
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 6.3 Å / R factor R free: 0 / R factor R work: 0.519 / Lowest resolution: 6.463 Å / Number reflection R free: 0 / Number reflection R work: 7099 / Total number of bins used: 20 / Percent reflection obs: 1

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