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- PDB-5wlc: The complete structure of the small subunit processome -

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Entry
Database: PDB / ID: 5wlc
TitleThe complete structure of the small subunit processome
DescriptorrpS18_uS13
rpS4_eS4
rpS5_uS7
rpS6_eS6
rpS7_eS7
and more 58 items
KeywordsRIBOSOME / Ribosome assembly
Specimen sourceSaccharomyces cerevisiae by4741 / yeast / Baker's yeast / image: Saccharomyces cerevisiae
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsBarandun, J. / Chaker-Margot, M. / Hunziker, M. / Klinge, S.
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 Yorodumi Papers
The complete structure of the small-subunit processome.
Jonas Barandun / Malik Chaker-Margot / Mirjam Hunziker / Kelly R Molloy / Brian T Chait / Sebastian Klinge

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2017 / Release: Sep 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 27, 2017Structure modelrepositoryInitial release
1.1Oct 11, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Oct 18, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

Deposited unit
L0: 5' ETS
L1: 18S pre-rRNA
L2: U3 snoRNA
L3: rpS18_uS13
L4: rpS4_eS4
L5: rpS5_uS7
L6: rpS6_eS6
L7: rpS7_eS7
L8: rpS8_eS8
L9: rpS9_uS4
LC: rpS16_uS9
LD: rpS11_uS17
LE: rpS22_uS8
LF: rpS24_eS24
LG: rpS28_eS28
LH: Utp17
LI: Utp8
LJ: Utp15
LK: Utp9
LL: Utp5
LM: Utp10
LN: Utp4
LO: Utp1
LP: Utp6
LQ: Utp12
LR: Utp13
LS: Utp18
LT: Utp21
LU: Sof1
LV: Enp2
LW: Utp7
LX: Kre33
LY: Kre33
LZ: Imp3
NA: Mpp10
NB: Sas10
NC: Lcp5
ND: Bud21
NE: Faf1
NF: rpS13_uS15
NG: rpS14_uS11
NH: Utp22
NI: Rrp7
NJ: Rrp5
NK: Krr1
SA: Nop56
SB: Nop58
SC: Nop1
SD: Nop1
SE: Snu13
SF: Snu13
SG: Rrp9
SH: Rcl1
SI: Bms1
SJ: Emg1
SK: Emg1
SL: Utp24
SM: Imp4
SN: Utp30
SO: Pno1
SP: Utp20
SQ: Fcf2
SR: rpS23_uS12
SS: Utp14
ST: Nop14
SU: Noc4
SV: Rrt14
SX: Unassigned peptides
SY: Utp11
SZ: Enp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,499,17571
Polyers4,499,11070
Non-polymers651
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules L0L1L2

#1: RNA chain5' ETS


Mass: 225543.094 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: GenBank: 1262303
#2: RNA chain18S pre-rRNA


Mass: 582052.438 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: GenBank: 874346701
#3: RNA chainU3 snoRNA


Mass: 106503.258 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: GenBank: 176452

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Polypeptide(L) , 63 types, 67 molecules L3L4L5L6L7L8L9LCLDLE...

#4: Polypeptide(L)rpS18_uS13


Mass: 16773.332 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CX55
#5: Polypeptide(L)rpS4_eS4


Mass: 29469.330 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CX35
#6: Polypeptide(L)rpS5_uS7


Mass: 25072.600 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: A0A1L4AA68
#7: Polypeptide(L)rpS6_eS6


Mass: 27054.486 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CX37
#8: Polypeptide(L)rpS7_eS7


Mass: 21658.209 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P26786
#9: Polypeptide(L)rpS8_eS8


Mass: 22537.803 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CX39
#10: Polypeptide(L)rpS9_uS4


Mass: 22487.893 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: O13516
#11: Polypeptide(L)rpS16_uS9


Mass: 15877.490 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CX51
#12: Polypeptide(L)rpS11_uS17


Mass: 17785.934 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CX47
#13: Polypeptide(L)rpS22_uS8


Mass: 14650.062 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0C0W1
#14: Polypeptide(L)rpS24_eS24


Mass: 15362.848 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CX31
#15: Polypeptide(L)rpS28_eS28


Mass: 7605.847 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q3E7X9
#16: Polypeptide(L)Utp17


Mass: 100960.445 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q02931
#17: Polypeptide(L)Utp8


Mass: 65572.977 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P53276
#18: Polypeptide(L)Utp15


Mass: 57765.289 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q04305
#19: Polypeptide(L)Utp9


Mass: 64378.512 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P38882
#20: Polypeptide(L)Utp5


Mass: 72079.445 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q04177
#21: Polypeptide(L)Utp10


Mass: 200020.719 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P42945
#22: Polypeptide(L)Utp4


Mass: 87316.500 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q06679
#23: Polypeptide(L)Utp1


Mass: 104097.039 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P25635
#24: Polypeptide(L)Utp6


Mass: 48437.402 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q02354
#25: Polypeptide(L)Utp12


Mass: 105037.648 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q12220
#26: Polypeptide(L)Utp13


Mass: 75035.867 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q05946
#27: Polypeptide(L)Utp18


Mass: 66494.250 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P40362
#28: Polypeptide(L)Utp21


Mass: 104927.844 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q06078
#29: Polypeptide(L)Sof1


Mass: 56888.918 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P33750
#30: Polypeptide(L)Enp2


Mass: 81864.172 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P48234
#31: Polypeptide(L)Utp7


Mass: 62418.570 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P40055
#32: Polypeptide(L)Kre33


Mass: 95337.062 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P53914, EC: 2.3.1.-
#33: Polypeptide(L)Imp3


Mass: 21928.529 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P32899
#34: Polypeptide(L)Mpp10


Mass: 67042.492 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P47083
#35: Polypeptide(L)Sas10


Mass: 69705.703 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q12136
#36: Polypeptide(L)Lcp5


Mass: 40864.391 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P40079
#37: Polypeptide(L)Bud21


Mass: 23835.627 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q08492
#38: Polypeptide(L)Faf1


Mass: 38173.699 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P40546
#39: Polypeptide(L)rpS13_uS15


Mass: 17059.945 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P05756
#40: Polypeptide(L)rpS14_uS11


Mass: 14562.655 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P06367
#41: Polypeptide(L)Utp22


Mass: 140660.141 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P53254
#42: Polypeptide(L)Rrp7


Mass: 34526.441 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P25368
#43: Polypeptide(L)Rrp5


Mass: 193411.422 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q05022
#44: Polypeptide(L)Krr1


Mass: 37226.254 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: B3LU25
#45: Polypeptide(L)Nop56


Mass: 56394.863 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q12460
#46: Polypeptide(L)Nop58


Mass: 53814.520 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q12499
#47: Polypeptide(L)Nop1


Mass: 34525.418 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P15646, EC: 2.1.1.-
#48: Polypeptide(L)Snu13


Mass: 13582.855 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P39990
#49: Polypeptide(L)Rrp9


Mass: 65146.969 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q06506
#50: Polypeptide(L)Rcl1


Mass: 40220.559 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q08096
#51: Polypeptide(L)Bms1


Mass: 135152.938 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q08965
#52: Polypeptide(L)Emg1


Mass: 27936.461 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q06287, EC: 2.1.1.260
#53: Polypeptide(L)Utp24


Mass: 21650.729 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q05498
#54: Polypeptide(L)Imp4


Mass: 33536.168 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P53941
#55: Polypeptide(L)Utp30


Mass: 31668.939 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P36144
#56: Polypeptide(L)Pno1


Mass: 30380.623 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q99216
#57: Polypeptide(L)Utp20


Mass: 83590.180 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741
#58: Polypeptide(L)Fcf2


Mass: 25689.240 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q12035
#59: Polypeptide(L)rpS23_uS12


Mass: 16073.896 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P0CY39
#60: Polypeptide(L)Utp14


Mass: 101101.461 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q04500
#61: Polypeptide(L)Nop14


Mass: 85993.961 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q99207
#62: Polypeptide(L)Noc4


Mass: 58369.125 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: Q06512
#63: Polypeptide(L)Rrt14


Mass: 21036.877 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: B5VKI1, UniProt: E9P9B2
#64: Polypeptide(L)Unassigned peptides


Mass: 8783.818 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741
#65: Polypeptide(L)Utp11


Mass: 29806.348 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: B5VM59
#66: Polypeptide(L)Enp1


Mass: 55207.422 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae BY4741 / References: UniProt: P38333

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Non-polymers , 1 types, 1 molecules

#67: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn

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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: Small subunit processome / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66
Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae BY4741
Buffer solutionpH: 7.7
Buffer component
IDConc.UnitsNameFormulaBuffer ID
150mMTris(HOCH2)3CNH21
2150mMsodium chlorideNaCl1
31mMEDTA(HO2CCH2)2NCH2CH2N(CH2CO2H)21
40.1%Triton X-1001
55mMbiotin1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 50 mA / Grid material: COPPER / Grid mesh size: 400 / Grid type: Ted Pella Inc.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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: 22500 / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 4 / Number of real images: 10029
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1RELION2PARTICLE SELECTION1
2SerialEMIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7Coot0.8.9MODEL FITTING1
9RELION2INITIAL EULER ASSIGNMENT1
10RELION2FINAL EULER ASSIGNMENT1
11RELION2CLASSIFICATION1
12RELION2RECONSTRUCTION1
13PHENIX1.12rc1MODEL REFINEMENT1
CTF correctionType: NONE
Particle selectionNumber of particles selected: 772120
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 284213 / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingOverall b value: 338.9 / Ref protocol: OTHER / Ref space: REAL

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