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- EMDB-8621: The cryo-EM structure of YjeQ bound to the 30S subunit suggests a... -

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Basic information

Entry
Database: EMDB / ID: 8621
TitleThe cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly
SampleStructure of the 30S subunit in complex with YjeQ GTPase
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataStructure of the mature 30S subunit in complex with YjeQ (RsgA) GTPase
Methodsingle particle reconstruction, at 5.8 Å resolution
AuthorsRazi A / Guarne A
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, E3396-E3403

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

Validation ReportPDB-ID: 5uz4

SummaryFull reportAbout validation report
DateDeposition: Feb 24, 2017 / Header (metadata) release: Apr 19, 2017 / Map release: Apr 19, 2017 / Last update: May 10, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0309
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.0309
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5uz4
  • Surface level: 0.0309
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8621.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.45 Å/pix.
= 319. Å
220 pix
1.45 Å/pix.
= 319. Å
220 pix
1.45 Å/pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:0.0309 (by author), 0.0309 (movie #1):
Minimum - Maximum-0.034293998 - 0.09952094
Average (Standard dev.)0.0011337413 (0.0060786973)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin000
Limit219219219
Spacing220220220
CellA=B=C: 319 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z319.000319.000319.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0340.1000.001

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Supplemental data

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Sample components

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Entire Structure of the 30S subunit in complex with YjeQ GTPase

EntireName: Structure of the 30S subunit in complex with YjeQ GTPase
Number of components: 24

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Component #1: protein, Structure of the 30S subunit in complex with YjeQ GTPase

ProteinName: Structure of the 30S subunit in complex with YjeQ GTPase
Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: nucleic-acid, 16S RIBOSOMAL RNA

Nucleic-acidName: 16S RIBOSOMAL RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAAGAGUUUG AUCAUGGCUC AGAUUGAACG CUGGCGGCAG GCCUAACACA UGCAAGUCGA ACGGUAACAG GAAGAAGCUU GCUUCUUUGC UGACGAGUGG CGGACGGGUG AGUAAUGUCU GGGAAACUGC CUGAUGGAGG GGGAUAACUA CUGGAAACGG UAGCUAAUAC CGCAUAACGU CGCAAGACCA AAGAGGGGGA CCUUCGGGCC UCUUGCCAUC GGAUGUGCCC AGAUGGGAUU AGCUAGUAGG UGGGGUAACG GCUCACCUAG GCGACGAUCC CUAGCUGGUC UGAGAGGAUG ACCAGCCACA CUGGAACUGA GACACGGUCC AGACUCCUAC GGGAGGCAGC AGUGGGGAAU AUUGCACAAU GGGCGCAAGC CUGAUGCAGC CAUGCCGCGU GUAUGAAGAA GGCCUUCGGG UUGUAAAGUA CUUUCAGCGG GGAGGAAGGG AGUAAAGUUA AUACCUUUGC UCAUUGACGU UACCCGCAGA AGAAGCACCG GCUAACUCCG UGCCAGCAGC CGCGGUAAUA CGGAGGGUGC AAGCGUUAAU CGGAAUUACU GGGCGUAAAG CGCACGCAGG CGGUUUGUUA AGUCAGAUGU GAAAUCCCCG GGCUCAACCU GGGAACUGCA UCUGAUACUA GCAAGCUUGA GUCUCGUAGA GGGGGGUAGA AUUCCAGGUG UAGCGGUGAA AUGCGUAGAG AUCUGGAGGA AUACCGGUGG CGAAGGCGGC CCCCUGGACG AAGACUGACG CUCAGGUGCG AAAGCGUGGG GAGCAAACAG GAUUAGAUAC CCUGGUAGUC CACGCCGUAA ACGAUGUCGA CUUGGAGGUU GUGCCCUUGA GGCGUGGCUU CCGGAGCUAA CGCGUUAAGU CGACCGCCUG GGGAGUACGG CCGCAAGGUU AAAACUCAAA UGAAUUGACG GGGGCCCGCA CAAGCGGUGG AGCAUGUGGU UUAAUUCGAU GCAACGCGAA GAACCUUACC UGGUCUUGAC AUCCACGGAA GUUUUCAGAG AUGAGAAUGU GCCUUCGGGA ACCGUGAGAC AGGUGCUGCA UGGCUGUCGU CAGCUCGUGU UGUGAAAUGU UGGGUUAAGU CCCGCAACGA GCGCAACCCU UAUCCUUUGU UGCCAGCGGU CCGGCCGGGA ACUCAAAGGA GACUGCCAGU GAUAAACUGG AGGAAGGUGG GGAUGACGUC AAGUCAUCAU GGCCCUUACG ACCAGGGCUA CACACGUGCU ACAAUGGCGC AUACAAAGAG AAGCGACCUC GCGAGAGCAA GCGGACCUCA UAAAGUGCGU CGUAGUCCGG AUUGGAGUCU GCAACUCGAC UCCAUGAAGU CGGAAUCGCU AGUAAUCGUG GAUCAGAAUG CCACGGUGAA UACGUUCCCG GGCCUUGUAC ACACCGCCCG UCACACCAUG GGAGUGGGUU GCAAAAGAAG UAGGUAGCUU AACCUUCGGG AGGGCGCUUA CCACUUUGUG AUUCAUGACU GGGGUGAAGU CGUAACAAGG UAACCGUAGG GGAACCUGCG GUUGGAU
MassTheoretical: 494.971188 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #4: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #5: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #6: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 15.211058 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #7: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 20.055156 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #8: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #9: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #10: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #11: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #12: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 13.768157 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #13: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #14: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #15: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 10.319882 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #16: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #17: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #18: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #19: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #20: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #21: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #22: protein, Small ribosomal subunit biogenesis GTPase RsgA

ProteinName: Small ribosomal subunit biogenesis GTPase RsgA / Recombinant expression: No
MassTheoretical: 37.345172 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #24: ligand, 3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-...

LigandName: 3'-O-(N-methylanthraniloyl)-beta:gamma-imidoguanosine-5'-triphosphate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.655343 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000 X (nominal), 34482 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 130462
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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