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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 Å resolution / Particle / Single particle)
AuthorsRazi, A. / Guarne, A. / Ortega, J.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, E3396-E3403

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E3396-E3403 Yorodumi Papers
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 24, 2017 / Release: Apr 19, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 19, 2017Structure modelrepositoryInitial release
1.1Apr 26, 2017Structure modelDatabase references
1.2May 10, 2017Structure modelDatabase references
1.3Sep 27, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

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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

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCR2

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: P0A7W3

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MCS2

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein S15


Mass: 10319.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: Q8X9M2

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MIU7

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli / References: UniProt: B7MAE3

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein S2


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

Cellular component

Molecular function

Biological process

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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.-

Cellular component

Molecular function

Biological process

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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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Structure of the 30S subunit in complex with YjeQ GTPase
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
Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: C-flat CFT-222C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
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 / Calibrated magnification: 34482 / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2 mm / C2 aperture diameter: 50 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 0.5 sec. / Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30 / Used frames/image: 1-20

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Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
9RELION1.4INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
11RELION1.4CLASSIFICATION1
13CootMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 487018
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 130462 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER

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