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- EMDB-6790: Small subunit of Mycobacterium smegmatis ribosome -

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Basic information

Entry
Database: EMDB / ID: 6790
TitleSmall subunit of Mycobacterium smegmatis ribosome
Map data
SampleSmall subunit of Mycobacterium smegmatis ribosome:
nucleic-acidNucleic acid / (30S ribosomal protein ...) x 18 / Conserved domain proteinProtein domain / ligand
Function / homologyRibosomal protein S10 domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily ...Ribosomal protein S10 domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / Ribosomal protein S4/S9 N-terminal domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S15 / Ribosomal protein S6 superfamily / Ribosomal protein S16 signature. / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S19, superfamily / Ribosomal protein S14, type Z / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S6, conserved site / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S14p/S29e / Ribosomal protein S5, N-terminal domain / Ribosomal protein S16, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5 signature. / Ribosomal protein S3 signature. / Ribosomal protein S14 signature. / Ribosomal protein S15 signature. / Ribosomal protein S10 signature. / Ribosomal protein S9 signature. / Ribosomal protein S19 signature. / Ribosomal protein S18 signature. / Ribosomal protein S17 signature. / Ribosomal protein S12 signature. / Ribosomal protein S11 signature. / Ribosomal protein S8 signature. / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein S10p/S20e / KH domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S20 / S4 domain / Ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S16 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein S8 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S14 / K Homology domain / K Homology domain, type 2 / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S3, C-terminal / Ribosomal protein S5 / Ribosomal protein S5, C-terminal / Ribosomal protein S9 / Ribosomal protein S8 / Ribosomal protein S15 / Ribosomal protein S6 / Ribosomal protein S16 / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / 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. / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S3, bacterial / 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 S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S5, N-terminal, conserved site
Function and homology information
SourceMycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.45 Å resolution
AuthorsLi Z / Zhang Y
CitationJournal: Protein Cell / Year: 2018
Title: Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.
Authors: Zhifei Li / Xueliang Ge / Yixiao Zhang / Lvqin Zheng / Suparna Sanyal / Ning Gao
Validation ReportPDB-ID: 5xyu

SummaryFull reportAbout validation report
DateDeposition: Jul 10, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Sep 27, 2017 / Last update: Apr 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0446
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0446
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xyu
  • Surface level: 0.0446
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6790.map.gz (map file in CCP4 format, 87809 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
1.32 Å/pix.
= 369.6 Å
280 pix
1.32 Å/pix.
= 369.6 Å
280 pix
1.32 Å/pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.0446 (by author), 0.0446 (movie #1):
Minimum - Maximum-0.14852048 - 0.26202428
Average (Standard dev.)0.00040286453 (0.006934687)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin000
Limit279279279
Spacing280280280
CellA=B=C: 369.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1490.2620.000

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Supplemental data

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Sample components

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Entire Small subunit of Mycobacterium smegmatis ribosome

EntireName: Small subunit of Mycobacterium smegmatis ribosome / Number of components: 22

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Component #1: protein, Small subunit of Mycobacterium smegmatis ribosome

ProteinName: Small subunit of Mycobacterium smegmatis ribosome / Recombinant expression: No
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #2: nucleic-acid, 16S RNA

Nucleic-acidName: 16S RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUGUUUG GAGAGUUUGA UCCUGGCUCA GGACGAACGC UGGCGGCGUG CUUAACACAU GCAAGUCGAA CGGAAAGGCC CUUUCGGGGG UACUCGAGUG GCGAACGGGU GAGUAACACG UGGGUGAUCU GCCCUGCACU UUGGGAUAAG CCUGGGAAAC UGGGUCUAAU ACCGAAUACA CCCUGCUGGU CGCAUGGCCU GGUAGGGGAA AGCUUUUGCG GUGUGGGAUG GGCCCGCGGC CUAUCAGCUU GUUGGUGGGG UGAUGGCCUA CCAAGGCGAC GACGGGUAGC CGGCCUGAGA GGGUGACCGG CCACACUGGG ACUGAGAUAC GGCCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCGACGC CGCGUGAGGG AUGACGGCCU UCGGGUUGUA AACCUCUUUC AGCACAGACG AAGCGCAAGU GACGGUAUGU GCAGAAGAAG GACCGGCCAA CUACGUGCCA GCAGCCGCGG UAAUACGUAG GGUCCGAGCG UUGUCCGGAA UUACUGGGCG UAAAGAGCUC GUAGGUGGUU UGUCGCGUUG UUCGUGAAAA CUCACAGCUU AACUGUGGGC GUGCGGGCGA UACGGGCAGA CUAGAGUACU GCAGGGGAGA CUGGAAUUCC UGGUGUAGCG GUGGAAUGCG CAGAUAUCAG GAGGAACACC GGUGGCGAAG GCGGGUCUCU GGGCAGUAAC UGACGCUGAG GAGCGAAAGC GUGGGGAGCG AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGGU GGGUACUAGG UGUGGGUUUC CUUCCUUGGG AUCCGUGCCG UAGCUAACGC AUUAAGUACC CCGCCUGGGG AGUACGGCCG CAAGGCUAAA ACUCAAAGGA AUUGACGGGG GCCCGCACAA GCGGCGGAGC AUGUGGAUUA AUUCGAUGCA ACGCGAAGAA CCUUACCUGG GUUUGACAUG CACAGGACGC CGGCAGAGAU GUCGGUUCCC UUGUGGCCUG UGUGCAGGUG GUGCAUGGCU GUCGUCAGCU CGUGUCGUGA GAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUGUCU CAUGUUGCCA GCACGUUAUG GUGGGGACUC GUGAGAGACU GCCGGGGUCA ACUCGGAGGA AGGUGGGGAU GACGUCAAGU CAUCAUGCCC CUUAUGUCCA GGGCUUCACA CAUGCUACAA UGGCCGGUAC AAAGGGCUGC GAUGCCGUGA GGUGGAGCGA AUCCUUUCAA AGCCGGUCUC AGUUCGGAUC GGGGUCUGCA ACUCGACCCC GUGAAGUCGG AGUCGCUAGU AAUCGCAGAU CAGCAACGCU GCGGUGAAUA CGUUCCCGGG CCUUGUACAC ACCGCCCGUC ACGUCAUGAA AGUCGGUAAC ACCCGAAGCC GGUGGCCUAA CCCUUGUGGA GGGAGCCGUC GAAGGUGGGA UCGGCGAUUG GGACGAAGUC GUAACAAGGU AGCCGUACCG GAAGGUGCGG CUGGAUCACC UCCUUUCU
MassTheoretical: 495.373656 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #3: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Recombinant expression: No
MassTheoretical: 30.191227 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #4: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 23.415787 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #5: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Recombinant expression: No
MassTheoretical: 21.94609 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #6: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 10.200688 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #7: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Recombinant expression: No
MassTheoretical: 17.660375 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #8: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 14.492638 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #9: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Recombinant expression: No
MassTheoretical: 16.794365 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #10: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.454313 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #11: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Recombinant expression: No
MassTheoretical: 14.671762 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #12: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Recombinant expression: No
MassTheoretical: 13.896366 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #13: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Recombinant expression: No
MassTheoretical: 14.249619 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #14: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type ZRibosome / Recombinant expression: No
MassTheoretical: 6.976409 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #15: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Recombinant expression: No
MassTheoretical: 10.368097 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #16: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Recombinant expression: No
MassTheoretical: 16.795207 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #17: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Recombinant expression: No
MassTheoretical: 11.127002 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #18: protein, 30S ribosomal protein S18 2

ProteinName: 30S ribosomal protein S18 2Ribosome / Recombinant expression: No
MassTheoretical: 9.524188 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #19: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Recombinant expression: No
MassTheoretical: 10.800602 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #20: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Recombinant expression: No
MassTheoretical: 9.556104 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #21: protein, Conserved domain protein

ProteinName: Conserved domain proteinProtein domain / Recombinant expression: No
MassTheoretical: 4.1643 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155

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Component #22: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 48 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 47338
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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