[English] 日本語
Yorodumi
- PDB-6fec: Human cap-dependent 48S pre-initiation complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

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 / homologyeIF3 subunit M, C-terminal helix / RNA polymerase I-associated factor PAF67 / Ribosomal protein S30 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / Initiation factor eIF2 gamma, C terminal / eIF3 subunit 6 N terminal domain / CSN8/PSMD8/EIF3K family / 40S ribosomal protein S4 C-terminus ...eIF3 subunit M, C-terminal helix / RNA polymerase I-associated factor PAF67 / Ribosomal protein S30 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / Initiation factor eIF2 gamma, C terminal / eIF3 subunit 6 N terminal domain / CSN8/PSMD8/EIF3K family / 40S ribosomal protein S4 C-terminus / S25 ribosomal protein / 40S ribosomal protein SA C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ubiquitin domain signature. / Plectin/S10 domain / Elongation factor Tu domain 2 / Ribosomal protein S9 signature. / Ribosomal S3Ae family / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / KOW motif / Ribosomal S17 / Ribosomal family S4e / Ribosomal protein S6e / Ribosomal protein S27 / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S7e / Ribosomal protein S24e / PCI domain / S4 domain / Ribosomal protein S27a / Ribosomal protein S19 signature. / Ribosomal protein S10 signature. / Ribosomal protein S10p/S20e / Activation of NF-kappaB in B cells / Trp-Asp (WD) repeats circular profile. / Type-2 KH domain profile. / S4 RNA-binding domain profile. / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / ISG15 antiviral mechanism / Ribosomal protein S13 family profile. / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / ER-Phagosome pathway / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / L13a-mediated translational silencing of Ceruloplasmin expression / PCI domain profile. / Eukaryotic RNA Recognition Motif (RRM) profile. / Ribosomal protein S15 signature. / Ribosomal protein S17e signature. / Ribosomal protein S14 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S3 signature. / Ribosomal protein S6e signature. / Ribosomal protein S4 signature. / Ribosomal protein S13 signature. / Trp-Asp (WD) repeats signature. / Ribosomal protein S7e signature. / Trp-Asp (WD) repeats profile. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S27e signature. / Ribosomal protein S12e signature. / Ribosomal protein S3Ae signature. / Ribosomal protein S8e signature. / Ubiquitin domain profile. / Ribosomal protein S17 / Ribosomal protein S2 / Budding and maturation of HIV virion / Ubiquitin / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Translation initiation factor 3 complex subunit L / WD40 repeat, conserved site / Ubiquitin conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S17e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.3 Å resolution
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
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
1.2Oct 3, 2018Structure modelData collection / Refinement descriptioncomputing / refine

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4242
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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 (human)
#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 (human) / 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 (human) / 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 (human) / Cell line: Hela / References: 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human)
#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 (human) / 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 (human) / 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 (human)
#49: Protein/peptide Eukaryotic translation initiation factor 4B / eIF-4B


Mass: 72324.820 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4B / Plasmid name: pFastBac_eIF4B / Production host: Spodoptera frugiperda (fall armyworm) / 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 (human) / Cell line: hela

-
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 (human) / Cell line: hela
#11: RNA chain Messenger RNA (26-MER)


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


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

+
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 (human) / 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 (human) / Cell line: hela / References: UniProt: P62249
#14: Protein/peptide 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29658.920 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / Cell line: hela
References: UniProt: P23396, 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / 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 (human) / Cell line: hela / References: UniProt: P46783

-
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 (human) / 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 (human) / Cell line: hela / References: UniProt: P62979

-
Non-polymers , 1 types, 415 molecules

#51: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
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: 2.0 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
239606Homo sapiens (human)
349606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
13562Escherichia coli (E. coli)
247108Spodoptera frugiperda (fall armyworm)
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

-
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 FIELDBright-field microscopy / 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)

-
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
13RELION1.43D reconstruction
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
RefineCorrelation coeff Fo to Fc: 0.961 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 135.967 / Overall SU ML: 0.877
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso mean: 105.458 Å2 / Aniso B11: 0.64 Å2 / Aniso B12: -0.57 Å2 / Aniso B13: -1.05 Å2 / Aniso B22: 4.34 Å2 / Aniso B23: -2.56 Å2 / Aniso B33: -4.98 Å2
Least-squares processR factor R work: 0.37479 / R factor obs: 0.37479 / Highest resolution: 6.3 Å / Lowest resolution: 27 Å / Number reflection obs: 95026 / Percent reflection obs: 1
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

+
About Yorodumi

-
News

-
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

-
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

+
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

+
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

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

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

Read more