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- PDB-5uz4: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a... -

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Entry
Database: PDB / ID: 5uz4
TitleThe cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly
Descriptor30S Ribosome
KeywordsRIBOSOME/Hydrolase / Ribosome assembly / 30S subunit / YjeQ protein / RsgA protein / RIBOSOME-Hydrolase complex
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (5.8 A resolution / Single particle)
AuthorsRazi, A. / Guarne, A. / Ortega, J.
CitationProc. Natl. Acad. Sci. U.S.A., 2017

Proc. Natl. Acad. Sci. U.S.A., 2017 StrPapers
The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.
Aida Razi / Alba Guarné / Joaquin Ortega

DateDeposition: Feb 24, 2017 / Release: Apr 19, 2017 / Last modification: Apr 26, 2017

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Assembly

Deposited unit
A: 16S RIBOSOMAL RNA
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
B: 30S ribosomal protein S2
Z: Small ribosomal subunit biogenesis GTPase RsgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)813,84423
Polyers813,12321
Non-polymers7212
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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30S ribosomal protein ... , 19 types, 19 molecules CDEFGHIJKL...

#2: Polypeptide(L)30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCS9
#3: Polypeptide(L)30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCR2
#4: Polypeptide(L)30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7W3
#5: Polypeptide(L)30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 15211.058 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02358
#6: Polypeptide(L)30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P02359
#7: Polypeptide(L)30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCS1
#8: Polypeptide(L)30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MBZ1
#9: Polypeptide(L)30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCT6
#10: Polypeptide(L)30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCR3
#11: Polypeptide(L)30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCV7
#12: Polypeptide(L)30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7T1
#13: Polypeptide(L)30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCS2
#14: Polypeptide(L)30S ribosomal protein S15


Mass: 10319.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: Q8X9M2
#15: Polypeptide(L)30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MIU7
#16: Polypeptide(L)30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCS6
#17: Polypeptide(L)30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MLK7
#18: Polypeptide(L)30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCT1
#19: Polypeptide(L)30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MAE3
#20: Polypeptide(L)30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MBF0

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RNA chain / Polypeptide(L) , 2 types, 2 molecules AZ

#1: RNA chain16S RIBOSOMAL RNA


Mass: 494971.188 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: GenBank: 1095872043
#21: Polypeptide(L)Small ribosomal subunit biogenesis GTPase RsgA


Mass: 37345.172 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P39286, EC: 3.6.1.-

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Non-polymers , 2 types, 2 molecules

#22: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn
#23: ChemicalChemComp-GGM / 3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-triphosphate / MANT-GMPPNP


Mass: 655.343 Da / Num. of mol.: 1 / Formula: C18H24N7O14P3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Structure of the 30S subunit in complex with YjeQ GTPase
Type: COMPLEX
Specimen supportGrid material: COPPER / Grid mesh size: 200 /inch. / Grid type: C-flat CFT-222C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 25000 X / Calibrated magnification: 34482 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER

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Processing

3D reconstructionResolution: 5.8 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 130462
Atomic model buildingRef protocol: OTHER

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