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- PDB-5oql: Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum -

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Entry
Database: PDB / ID: 5oql
TitleCryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum
KeywordsRIBOSOME / Ribosome biogenesis
Specimen sourceChaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) / fungus
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsCheng, J. / Kellner, N. / Berninghausen, O. / Hurt, E. / Beckmann, R.
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 Yorodumi Papers
3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage.
Jingdong Cheng / Nikola Kellner / Otto Berninghausen / Ed Hurt / Roland Beckmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 12, 2017 / Release: Oct 11, 2017

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Assembly

Deposited unit
A: Periodic tryptophan protein 2-like protein
B: Utp2
C: Utp3
D: Utp4
E: Utp6
F: Utp7
G: Utp10
H: U3 small nucleolar RNA-associated protein 11
I: Utp12
J: Utp13
K: Utp14
L: Utp15
M: Utp17
N: Utp18
O: Putative U3 snoRNP protein
P: Utp24
Q: Utp30
R: Nop1
S: Nop1
T: Putative nucleolar protein
U: Nop58
V: Snu13
W: Snu13
X: Rrp9
Y: RNA 3'-terminal phosphate cyclase-like protein
Z: Bms1
a: Imp3
b: Putative U3 small nucleolar ribonucleoprotein
c: Putative U3 small nucleolar ribonucleoprotein protein
d: Sof1
e: Emg1
f: Emg1
g: KRR1 small subunit processome component
h: Pre-rRNA-processing protein PNO1
i: RNA cytidine acetyltransferase
j: RNA cytidine acetyltransferase
k: Fcf2
l: 40S ribosomal protein S1
m: 40S ribosomal protein S4
n: 40S ribosomal protein s5-like protein
o: 40S ribosomal protein S6
p: 40S ribosomal protein S7-like protein
q: 40S ribosomal protein S8
r: 40S ribosomal protein s9-like protein
s: 40S ribosomal protein S13-like protein
t: 40S ribosomal protein S14-like protein
u: 40S ribosomal protein S16-like protein
v: 40S ribosomal protein S11-like protein
w: 40S ribosomal protein S22-like protein
x: 40S ribosomal protein s23-like protein
y: 40S ribosomal protein S24
z: 40S ribosomal protein S28-like protein
0: Faf1
1: 35S rRNA
2: U3 snoRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,735,32556
Polyers3,735,26055
Non-polymers651
Water0
#1


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

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Components

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Polypeptide(L) , 32 types, 36 molecules ABCDEFGHIJ...

#1: Polypeptide(L)Periodic tryptophan protein 2-like protein / Utp1


Mass: 100817.508 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SF93
#2: Polypeptide(L)Utp2


Mass: 103960.703 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SDW0
#3: Polypeptide(L)Utp3


Mass: 73214.633 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S4H3
#4: Polypeptide(L)Utp4


Mass: 97696.523 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SCT7
#5: Polypeptide(L)Utp6


Mass: 46924.773 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S387
#6: Polypeptide(L)Utp7


Mass: 63629.379 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RZ99
#7: Polypeptide(L)Utp10


Mass: 198508.438 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S5L1
#8: Polypeptide(L)U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / Utp11


Mass: 31379.650 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SF32
#9: Polypeptide(L)Utp12


Mass: 107573.039 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RZL9
#10: Polypeptide(L)Utp13


Mass: 100430.352 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SG95
#11: Polypeptide(L)Utp14


Mass: 104741.391 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S8Y4
#12: Polypeptide(L)Utp15


Mass: 60524.145 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SEI5
#13: Polypeptide(L)Utp17


Mass: 105039.695 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SCS8
#14: Polypeptide(L)Utp18


Mass: 69055.141 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SBN9
#15: Polypeptide(L)Putative U3 snoRNP protein / Utp21


Mass: 115122.008 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S872
#16: Polypeptide(L)Utp24


Mass: 22267.188 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SE30
#17: Polypeptide(L)Utp30


Mass: 43700.527 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S7X0
#18: Polypeptide(L)Nop1


Mass: 32960.844 Da / Num. of mol.: 2
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SGY2
#19: Polypeptide(L)Putative nucleolar protein / Nop56


Mass: 57830.699 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S2U4
#20: Polypeptide(L)Nop58


Mass: 64292.113 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RYF6
#21: Polypeptide(L)Snu13


Mass: 13831.854 Da / Num. of mol.: 2
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SGM0
#22: Polypeptide(L)Rrp9


Mass: 69610.438 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SG51
#23: Polypeptide(L)RNA 3'-terminal phosphate cyclase-like protein / Rcl1


Mass: 43399.766 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S0B1
#24: Polypeptide(L)Bms1


Mass: 134172.250 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S445
#25: Polypeptide(L)Imp3


Mass: 21802.396 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SDL4
#28: Polypeptide(L)Sof1


Mass: 50869.828 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RY94
#29: Polypeptide(L)Emg1


Mass: 27936.164 Da / Num. of mol.: 2
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SAY9
#30: Polypeptide(L)KRR1 small subunit processome component / KRR-R motif-containing protein 1


Mass: 37500.777 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S3V7
#31: Polypeptide(L)Pre-rRNA-processing protein PNO1 / Dim2


Mass: 28715.047 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S3T2
#32: Polypeptide(L)RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase / Kre33


Mass: 119795.125 Da / Num. of mol.: 2
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S273, EC: 2.3.1.-
#33: Polypeptide(L)Fcf2


Mass: 22569.129 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S4E3
#49: Polypeptide(L)Faf1


Mass: 34576.586 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S5F1

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Putative U3 small nucleolar ... , 2 types, 2 molecules bc

#26: Polypeptide(L)Putative U3 small nucleolar ribonucleoprotein / Imp4


Mass: 34216.266 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SE90
#27: Polypeptide(L)Putative U3 small nucleolar ribonucleoprotein protein / Mpp10


Mass: 86082.141 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S9I7

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40S ribosomal protein ... , 15 types, 15 molecules lmnopqrstu...

#34: Polypeptide(L)40S ribosomal protein S1 / eS1


Mass: 29245.158 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S7T8
#35: Polypeptide(L)40S ribosomal protein S4 / eS4


Mass: 29800.764 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S1A6
#36: Polypeptide(L)40S ribosomal protein s5-like protein / uS7


Mass: 23679.225 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S1Z0
#37: Polypeptide(L)40S ribosomal protein S6 / eS6


Mass: 27490.139 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RY43
#38: Polypeptide(L)40S ribosomal protein S7-like protein / eS7


Mass: 23084.650 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S8C4
#39: Polypeptide(L)40S ribosomal protein S8 / eS8


Mass: 23102.416 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RY45
#40: Polypeptide(L)40S ribosomal protein s9-like protein / uS4


Mass: 22029.836 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S0Z4
#41: Polypeptide(L)40S ribosomal protein S13-like protein / uS15


Mass: 16912.891 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RZM9
#42: Polypeptide(L)40S ribosomal protein S14-like protein


Mass: 16071.464 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SFL1
#43: Polypeptide(L)40S ribosomal protein S16-like protein / uS9


Mass: 15962.771 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SBR7
#44: Polypeptide(L)40S ribosomal protein S11-like protein / eS17


Mass: 18698.182 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SF00
#45: Polypeptide(L)40S ribosomal protein S22-like protein / uS8


Mass: 14905.471 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0SHI0
#46: Polypeptide(L)40S ribosomal protein s23-like protein / uS12


Mass: 15934.653 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0RY17
#47: Polypeptide(L)40S ribosomal protein S24 / eS24


Mass: 15535.286 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: P0CU28
#48: Polypeptide(L)40S ribosomal protein S28-like protein / eS28


Mass: 7741.980 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
References: UniProt: G0S9M9

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RNA chain , 2 types, 2 molecules 12

#50: RNA chain35S rRNA


Mass: 827801.812 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
#51: RNA chainU3 snoRNA


Mass: 87992.648 Da / Num. of mol.: 1
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

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Non-polymers , 1 types, 1 molecules

#52: 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: The 90S Pre-ribosomne / 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
Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
1Gautomatch0.50PARTICLE SELECTION1
4CTFFIND4CTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
8CootMODEL FITTING1
10RELION2.0INITIAL EULER ASSIGNMENT1
11RELION2.0FINAL EULER ASSIGNMENT1
12RELION2.0CLASSIFICATION1
13RELION2.0RECONSTRUCTION1
14PHENIXMODEL REFINEMENT1
15REFMACMODEL REFINEMENT1
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 231121 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007140858
ELECTRON MICROSCOPYf_angle_d1.137198388
ELECTRON MICROSCOPYf_dihedral_angle_d14.15181369
ELECTRON MICROSCOPYf_chiral_restr0.05924284
ELECTRON MICROSCOPYf_plane_restr0.00819361

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