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- PDB-4v91: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES -

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Basic information

Entry
Database: PDB / ID: 4v91
TitleKluyveromyces lactis 80S ribosome in complex with CrPV-IRES
DescriptorRibosome
KeywordsRIBOSOME / TRANSLATION / INITIATION / IRES
Specimen sourceKluyveromyces lactis / yeast
MethodElectron microscopy (3.7 Å resolution / Particle / Single particle)
AuthorsFernandez, I.S. / Bai, X. / Scheres, S.H.W. / Ramakrishnan, V.
CitationCell, 2014, 157, 823-831

Cell, 2014, 157, 823-831 Yorodumi Papers
Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome.
Israel S Fernández / Xiao-Chen Bai / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 21, 2014 / Release: Jul 9, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Apr 22, 2015Structure modelOther
2.0Aug 2, 2017Structure modelAdvisory / Atomic model / Data collection / Derived calculationsatom_site / em_software / pdbx_unobs_or_zero_occ_atoms / struct_conn_atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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Structure visualization

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Assembly

Deposited unit
1: 25S RRNA
3: 5S RRNA
4: 5.8S RRNA
A: UL2
B: UL3
C: UL4
D: UL18
E: EL6
F: UL30
G: EL8
H: UL6
I: UL16
J: UL5
L: EL13
M: EL14
N: EL15
O: UL13
P: UL22
Q: EL18
R: EL19
S: EL20
T: EL21
U: EL22
V: UL14
W: EL24
X: UL23
Y: UL24
Z: EL27
a: UL15
b: EL29
c: EL30
d: EL31
e: EL32
f: EL33
g: EL34
h: UL29
i: EL36
j: EL37
k: EL38
l: EL39
m: EL40
n: EL41
o: EL42
p: EL43
t: UL1


Theoretical massNumber of molelcules
Total (without water)1,977,85945
Polyers1,977,85945
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 134

#1: RNA chain25S RRNA


Mass: 1097866.125 Da / Num. of mol.: 1 / Source: (natural) KLUYVEROMYCES LACTIS
#2: RNA chain5S RRNA


Mass: 38951.105 Da / Num. of mol.: 1 / Source: (natural) KLUYVEROMYCES LACTIS
#3: RNA chain5.8S RRNA


Mass: 50682.922 Da / Num. of mol.: 1 / Source: (natural) KLUYVEROMYCES LACTIS

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Polypeptide(L) , 42 types, 42 molecules ABCDEFGHIJ...

#4: Polypeptide(L)UL2


Mass: 27463.574 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL2 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)UL3


Mass: 43850.793 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL3 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)UL4


Mass: 39159.125 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL4 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)UL18


Mass: 33764.828 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL18 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)EL6


Mass: 20000.564 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL6 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)UL30


Mass: 27686.281 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL30 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

  • cytoplasmic translation (GO: 0002181)
  • maturation of LSU-rRNA (GO: 0000470)
  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • ribosomal large subunit biogenesis (GO: 0042273)
#10: Polypeptide(L)EL8


Mass: 28175.820 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL8 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)UL6


Mass: 21605.061 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL6 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)UL16


Mass: 25410.465 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL16 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)UL5


Mass: 19755.691 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL5 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)EL13


Mass: 22604.164 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL13 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)EL14


Mass: 15195.066 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL14 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)EL15


Mass: 24482.357 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL15 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)UL13


Mass: 44476.383 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL13 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)UL22


Mass: 20589.518 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL2 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
#19: Polypeptide(L)EL18


Mass: 20609.252 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL18 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)EL19


Mass: 21762.316 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL19 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)EL20


Mass: 20478.852 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL20 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)EL21


Mass: 18279.266 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL21 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)EL22


Mass: 13711.359 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL22 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)UL14


Mass: 14493.950 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL14 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)EL24


Mass: 17661.717 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL24 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)UL23


Mass: 15787.612 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL23 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)UL24


Mass: 14265.784 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL24 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)EL27


Mass: 15568.360 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL27 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)UL15


Mass: 16761.666 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL15 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)EL29


Mass: 6691.884 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL29 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)EL30


Mass: 11430.364 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL30 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)EL31


Mass: 12980.158 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL31 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)EL32


Mass: 14809.441 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL32 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)EL33


Mass: 12177.130 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL33 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)EL34


Mass: 13673.196 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL34 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)UL29


Mass: 13942.640 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL29 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)EL36


Mass: 11151.259 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL36 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)EL37


Mass: 9877.395 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL37 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000448)
  • cytoplasmic translation (GO: 0002181)
  • translation (GO: 0006412)
#39: Polypeptide(L)EL38


Mass: 8845.561 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL38 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)EL39


Mass: 6358.640 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL39 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)EL40


Mass: 14583.077 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL40 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)EL41


Mass: 3354.243 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL41 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)EL42


Mass: 12246.658 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL42 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)EL43


Mass: 10112.952 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN EL43 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)UL1


Mass: 24524.799 Da / Num. of mol.: 1 / Details: RIBOSOMAL PROTEIN UL1 / Source: (natural) KLUYVEROMYCES LACTIS

Cellular component

Molecular function

Biological process

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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

ComponentName: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES
Type: RIBOSOME
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: PROPANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Jul 7, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 / Nominal defocus max: 3 nm / Nominal defocus min: 1.8 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNumber digital images: 1900
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
1REFMACMODEL FITTING1
2UCSF ChimeraMODEL FITTING1
3RELIONRECONSTRUCTION1
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1
3D reconstructionMethod: RELION / Resolution: 3.7 Å / Number of particles: 18132 / Nominal pixel size: 1.34 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--FLEXIBLE / Overall b value: 60 / Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: R-FACTOR, FSC
Atomic model buildingPDB-ID: 3B31
Least-squares processHighest resolution: 3.7 Å
Refine hist #LASTHighest resolution: 3.7 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 74446 / Ligand: 0 / Solvent: 0 / Total: 74446

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