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- PDB-3j80: CryoEM structure of 40S-eIF1-eIF1A preinitiation complex -

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Entry
Database: PDB / ID: 3j80
TitleCryoEM structure of 40S-eIF1-eIF1A preinitiation complex
Components
  • 18S rRNA18S ribosomal RNA
  • RACK1Receptor for activated C kinase 1
  • eIF1
  • eIF1A
  • eL41
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / small ribosome subunit / eukaryotic translation initiation
Function / homologyRibosomal protein S10 domain / Ribosomal protein S3, C-terminal domain superfamily / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily ...Ribosomal protein S10 domain / Ribosomal protein S3, C-terminal domain superfamily / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S7 domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain superfamily / SUI1 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S21e superfamily / S27a-like superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S2, eukaryotic / Ribosomal protein S7 domain / Ribosomal protein S7p/S5e / Ribosomal protein S8e, conserved site / Ribosomal S11, conserved site / Translation initiation factor 1A (eIF-1A), conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / WD40 repeat, conserved site / Ribosomal protein S2, flavodoxin-like domain superfamily / Ubiquitin conserved site / Ubiquitin / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S12/S23 / Ribosomal protein S3, C-terminal domain / Trp-Asp (WD) repeats signature. / Ribosomal protein S11 signature. / S25 ribosomal protein / Plectin/S10 domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / Ribosomal protein L41 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S12 signature. / Ribosomal protein S27a / Ribosomal protein S17 signature. / Ubiquitin domain signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S3 signature. / Ribosomal protein S6e signature. / Ribosomal protein S5 signature. / Ribosomal protein S19e signature. / Ribosomal protein S4 signature. / Ribosomal protein S27 / S4 domain / Ribosomal protein S19 / KOW motif / Ubiquitin family / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S10p/S20e / Ribosomal protein S17 / Ribosomal protein S9/S16
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
Kluyveromyces lactis (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.75 Å resolution
AuthorsHussain, T. / Llacer, J.L. / Fernandez, I.S. / Savva, C.G. / Ramakrishnan, V.
CitationJournal: Cell / Year: 2014
Title: Structural changes enable start codon recognition by the eukaryotic translation initiation complex.
Authors: Tanweer Hussain / Jose L Llácer / Israel S Fernández / Antonio Munoz / Pilar Martin-Marcos / Christos G Savva / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 28, 2014 / Release: Nov 5, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 5, 2014Structure modelrepositoryInitial release
1.1Dec 24, 2014Structure modelDatabase references
1.2Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id / _em_software.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
2: 18S rRNA
A: uS2
B: eS1
C: uS5
E: eS4
G: eS6
H: eS7
I: eS8
J: uS4
L: uS17
N: uS15
O: uS11
V: eS21
W: uS8
X: uS12
Y: eS24
a: eS26
b: eS27
e: eS30
D: uS3
F: uS7
K: eS10
M: eS12
P: uS19
Q: uS9
R: eS17
S: uS13
T: eS19
U: uS10
Z: eS25
c: eS28
d: uS14
f: eS31
g: RACK1
h: eL41
i: eIF1A
j: eIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,208,132107
Polyers1,206,30737
Non-polymers1,82570
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 579545.875 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast)

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Protein/peptide , 36 types, 36 molecules ABCEGHIJLNOVWXYabeDFKMPQRSTUZc...

#2: Protein/peptide uS2


Mass: 28264.525 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CN12
#3: Protein/peptide eS1


Mass: 28971.643 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWD0
#4: Protein/peptide uS5


Mass: 27649.979 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#5: Protein/peptide eS4


Mass: 29617.514 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWJ2
#6: Protein/peptide eS6


Mass: 26970.391 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#7: Protein/peptide eS7


Mass: 21735.297 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#8: Protein/peptide eS8


Mass: 22642.727 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CMG3
#9: Protein/peptide uS4


Mass: 21587.049 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#10: Protein/peptide uS17


Mass: 17843.930 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#11: Protein/peptide uS15


Mass: 16989.875 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#12: Protein/peptide uS11


Mass: 14530.655 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P27069
#13: Protein/peptide eS21


Mass: 9797.949 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXT6
#14: Protein/peptide uS8


Mass: 14645.041 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW21
#15: Protein/peptide uS12


Mass: 16047.897 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: F2Z602
#16: Protein/peptide eS24


Mass: 15194.549 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#17: Protein/peptide eS26


Mass: 13539.957 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#18: Protein/peptide eS27


Mass: 8884.362 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNL2
#19: Protein/peptide eS30


Mass: 7141.421 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5
#20: Protein/peptide uS3


Mass: 26300.535 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#21: Protein/peptide uS7


Mass: 25385.975 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#22: Protein/peptide eS10


Mass: 12584.377 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#23: Protein/peptide eS12


Mass: 14466.398 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLU4
#24: Protein/peptide uS19


Mass: 15768.522 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#25: Protein/peptide uS9


Mass: 15874.531 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875N2
#26: Protein/peptide eS17


Mass: 15722.216 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#27: Protein/peptide uS13


Mass: 17084.602 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#28: Protein/peptide eS19


Mass: 15879.010 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#29: Protein/peptide uS10


Mass: 13337.604 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#30: Protein/peptide eS25


Mass: 12002.116 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#31: Protein/peptide eS28


Mass: 7549.824 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P33285
#32: Protein/peptide uS14


Mass: 6662.570 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3
#33: Protein/peptide eS31


Mass: 17110.977 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#34: Protein/peptide RACK1 / Receptor for activated C kinase 1


Mass: 35830.945 Da / Num. of mol.: 1 / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7
#35: Protein/peptide eL41


Mass: 3354.243 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P0CX86
#36: Protein/peptide eIF1A


Mass: 17462.168 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P38912
#37: Protein/peptide eIF1 /


Mass: 12330.147 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P32911

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Non-polymers , 2 types, 70 molecules

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


Mass: 24.305 Da / Num. of mol.: 67 / Formula: Mg / Magnesium
#39: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Formula: Zn / Zinc

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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
IDNameTypeParent ID
140S-eIF1-eIF1A preinitiation complexCOMPLEX0
2Ribosome small subunitRIBOSOME1
3Eukaryotic initiation factor 11
4Eukaryotic initiation factor 1A1
Molecular weightValue: 1.2 MDa / Experimental value: NO
Buffer solutionName: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
Details: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT
pH: 6.5
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 %
Details: Blot for 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK I)
Method: Blot for 2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300 / Date: Oct 28, 2013
Details: Complete dataset was collected in 5 non-consecutive days
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: 4000 nm / Nominal defocus min: 1600 nm / Cs: 2 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNumber digital images: 1791
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0077 2014/05/16 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1REFMACmodel fitting
2UCSF Chimeramodel fitting
3EMAN23D reconstruction
4RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 100709 / Nominal pixel size: 1.34 / Actual pixel size: 1.34 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--flexible / Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: R-factor, FSC
Atomic model building
IDPDB-IDPdb chain ID 3D fitting ID
13U5B21
23U5C1
RefineDetails: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
Number of atoms included #LASTProtein: 39871 / Nucleic acid: 37775 / Ligand: 70 / Solvent: 0 / Total: 77716

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