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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
Components
  • (30S ribosomal protein ...) x 19
  • 16S RIBOSOMAL RNA
  • Small ribosomal subunit biogenesis GTPase RsgA
KeywordsRIBOSOME/Hydrolase / Ribosome assembly / 30S subunit / YjeQ protein / RsgA protein / RIBOSOME-Hydrolase complex
Function / homologyRibosomal protein S14, bacterial/plastid / Ribosomal protein S14, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S14, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / 30S ribosomal protein S17 / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S17, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S5 domain 2-type fold, subgroup / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5, N-terminal / Nucleic acid-binding, OB-fold / Ribosomal protein S13-like, H2TH / RsgA GTPase domain / S15/NS1, RNA-binding / Ribosomal protein S4/S9 / Ribosomal protein S16 / Ribosomal protein S12/S23 / RNA-binding S4 domain superfamily / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein S14p/S29e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S11 superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S6 superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / K homology domain superfamily, prokaryotic type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13/S18 / Ribosomal protein S14 signature. / RsgA GTPase / Ribosomal protein S5, C-terminal domain / KH domain / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S18 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S10 signature. / Ribosomal protein S15 signature. / Ribosomal protein S3 signature. / S4 domain / Ribosomal protein S5 signature. / Ribosomal protein S4 signature. / Ribosomal protein S13 signature. / Ribosomal protein S16 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S6 signature. / Ribosomal protein S13 family profile. / Type-2 KH domain profile. / S5 double stranded RNA-binding domain profile. / S4 RNA-binding domain profile. / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S20 / Ribosomal protein S6 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11 / Ribosomal protein S5, bacterial-type
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.8 Å resolution
AuthorsRazi, A. / Guarne, A. / Ortega, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.
Authors: 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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Structure visualization

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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 CDEFGHIJKLMNOPQRSTB

#2: Protein/peptide 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS9, UniProt: P0A7V3*PLUS
#3: Protein/peptide 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR2, UniProt: P0A7V8*PLUS
#4: Protein/peptide 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W3, UniProt: P0A7W1*PLUS
#5: Protein/peptide 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


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


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


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


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


Mass: 11755.597 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT6, UniProt: P0A7R5*PLUS
#10: Protein/peptide 30S ribosomal protein S11 /


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


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


Mass: 13128.467 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T1, UniProt: P0A7S9*PLUS
#13: Protein/peptide 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS2, UniProt: P0AG59*PLUS
#14: Protein/peptide 30S ribosomal protein S15 /


Mass: 10319.882 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q8X9M2, UniProt: P0ADZ4*PLUS
#15: Protein/peptide 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7, UniProt: P0A7T3*PLUS
#16: Protein/peptide 30S ribosomal protein S17 /


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


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


Mass: 10455.355 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCT1, UniProt: P0A7U3*PLUS
#19: Protein/peptide 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MAE3, UniProt: P0A7U7*PLUS
#20: Protein/peptide 30S ribosomal protein S2 /


Mass: 26781.670 Da / Num. of mol.: 1 / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MBF0, UniProt: P0A7V0*PLUS

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RNA chain / Protein/peptide , 2 types, 2 molecules AZ

#1: RNA chain 16S RIBOSOMAL RNA /


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


Mass: 37345.172 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rsgA, engC, yjeQ, b4161, JW4122 / Production host: Escherichia coli (E. coli)
References: UniProt: P39286, Hydrolases, Acting on acid anhydrides, In phosphorus-containing anhydrides

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Non-polymers , 2 types, 2 molecules

#22: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#23: Chemical ChemComp-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 reconstruction

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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 (E. 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 FIELDBright-field microscopy / Nominal magnification: 25000 / Calibrated magnification: 34482 / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2 mm / C2 aperture diameter: 50 microns / 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
IDNameVersionCategory
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
13Cootmodel refinement
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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