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- PDB-3j9w: Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome ... -

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Entry
Database: PDB / ID: 3j9w
TitleCryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex
DescriptorPROTEIN/RNA Complex
KeywordsRIBOSOME / stalling / translation arrest / mifm / L22
Specimen sourceBacillus subtilis subsp. subtilis str. 168 / bacteria / image: Bacillus subtilis
MethodElectron microscopy (3.9 Å resolution / Particle / Single particle)
AuthorsSohmen, D. / Chiba, S. / Shimokawa-Chiba, N. / Innis, C.A. / Berninghausen, O. / Beckmann, R. / Ito, K. / Wilson, D.N.
CitationNat Commun, 2015, 6, 6941-6941

Nat Commun, 2015, 6, 6941-6941 StrPapers
Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling.
Daniel Sohmen / Shinobu Chiba / Naomi Shimokawa-Chiba / C Axel Innis / Otto Berninghausen / Roland Beckmann / Koreaki Ito / Daniel N Wilson

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 16, 2015 / Release: Apr 29, 2015
RevisionDateData content typeGroupProviderType
1.0Apr 29, 2015Structure modelrepositoryInitial release
1.1May 6, 2015Structure modelDatabase references

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Assembly

Deposited unit
AA: 16S ribosomal RNA
AB: 30S ribosomal protein uS2
AC: 30S ribosomal protein uS3
AD: 30S ribosomal protein uS4
AE: 30S ribosomal protein uS5
AF: 30S ribosomal protein bS6
AG: 30S ribosomal protein uS7
AH: 30S ribosomal protein uS8
AI: 30S ribosomal protein uS9
AJ: 30S ribosomal protein uS10
AK: 30S ribosomal protein uS11
AL: 30S ribosomal protein uS12
AM: 30S ribosomal protein uS13
AN: 30S ribosomal protein uS14
AO: 30S ribosomal protein uS15
AP: 30S ribosomal protein bS16
AQ: 30S ribosomal protein uS17
AR: 30S ribosomal protein bS18
AS: 30S ribosomal protein uS19
AT: 30S ribosomal protein bS20
AX: tRNA-Asp
AY: mRNA
AZ: MifM
B0: 50S ribosomal protein bL28
B1: 50S ribosomal protein uL29
B2: 50S ribosomal protein uL30
B3: 50S ribosomal protein bL31
B4: 50S ribosomal protein bL32
B5: 50S ribosomal protein bL33
B6: 50S ribosomal protein bL34
B7: 50S ribosomal protein bL35
B8: 50S ribosomal protein bL36
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BD: 50S ribosomal protein uL2
BE: 50S ribosomal protein uL3
BF: 50S ribosomal protein uL4
BG: 50S ribosomal protein uL5
BH: 50S ribosomal protein uL6
BJ: 50S ribosomal protein uL10
BK: 50S ribosomal protein uL11
BM: 50S ribosomal protein uL13
BN: 50S ribosomal protein uL14
BO: 50S ribosomal protein uL15
BP: 50S ribosomal protein uL16
BQ: 50S ribosomal protein bL17
BR: 50S ribosomal protein uL18
BS: 50S ribosomal protein bL19
BT: 50S ribosomal protein bL20
BU: 50S ribosomal protein bL21
BV: 50S ribosomal protein uL22
BW: 50S ribosomal protein uL23
BX: 50S ribosomal protein uL24
BZ: 50S ribosomal protein bL27


Theoretical massNumber of molelcules
Total (without water)2,185,39954
Polyers2,185,39954
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules AAAXAYBABB

#1: RNA chain16S ribosomal RNA


Mass: 503698.281 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
#21: RNA chaintRNA-Asp


Mass: 24815.682 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
#22: RNA chainmRNA


Mass: 6204.786 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
#33: RNA chain23S ribosomal RNA


Mass: 949606.250 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
#34: RNA chain5S ribosomal RNA


Mass: 38423.863 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168

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

#2: Polypeptide(L)30S ribosomal protein uS2


Mass: 28009.297 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21464

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)30S ribosomal protein uS3


Mass: 24364.887 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21465

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)30S ribosomal protein uS4


Mass: 22874.271 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21466

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)30S ribosomal protein uS5


Mass: 17650.625 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21467

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein bS6


Mass: 11140.548 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21468

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)30S ribosomal protein uS7


Mass: 17915.879 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21469

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)30S ribosomal protein uS8


Mass: 14901.427 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12879

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)30S ribosomal protein uS9


Mass: 14335.504 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21470

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#10: Polypeptide(L)30S ribosomal protein uS10


Mass: 11687.661 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21471

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)30S ribosomal protein uS11


Mass: 13952.000 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P04969

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#12: Polypeptide(L)30S ribosomal protein uS12


Mass: 15248.736 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21472

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)30S ribosomal protein uS13


Mass: 13818.085 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P20282

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)30S ribosomal protein uS14


Mass: 7263.803 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12878

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)30S ribosomal protein uS15


Mass: 10597.224 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21473

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)30S ribosomal protein bS16


Mass: 10153.833 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21474

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)30S ribosomal protein uS17


Mass: 10220.979 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12874

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)30S ribosomal protein bS18


Mass: 8990.613 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21475

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)30S ribosomal protein uS19


Mass: 10607.309 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21476

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)30S ribosomal protein bS20


Mass: 9622.217 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P21477

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 1 types, 1 molecules AZ

#23: Polypeptide(L)MifM


Mass: 11156.958 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: Q7WY64

Cellular component

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50S ribosomal protein ... , 29 types, 29 molecules B0B1B2B3B4B5B6B7B8BD...

#24: Polypeptide(L)50S ribosomal protein bL28


Mass: 6826.144 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P37807

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)50S ribosomal protein uL29


Mass: 7728.029 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12873

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)50S ribosomal protein uL30


Mass: 6650.795 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P19947

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)50S ribosomal protein bL31


Mass: 7458.582 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: Q03223

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)50S ribosomal protein bL32


Mass: 6745.073 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: O34687

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)50S ribosomal protein bL33


Mass: 5915.875 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P56849

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)50S ribosomal protein bL34


Mass: 5271.332 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P05647

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)50S ribosomal protein bL35


Mass: 7581.128 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P55874

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)50S ribosomal protein bL36


Mass: 4318.422 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P20278

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)50S ribosomal protein uL2


Mass: 30335.125 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42919

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)50S ribosomal protein uL3


Mass: 22723.348 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42920

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)50S ribosomal protein uL4


Mass: 22424.951 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42921

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)50S ribosomal protein uL5


Mass: 20177.564 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12877

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)50S ribosomal protein uL6


Mass: 19543.389 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P46898

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)50S ribosomal protein uL10


Mass: 18101.748 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42923

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)50S ribosomal protein uL11


Mass: 14951.442 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: Q06796

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)50S ribosomal protein uL13


Mass: 16407.104 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P70974

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)50S ribosomal protein uL14


Mass: 13175.288 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12875

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)50S ribosomal protein uL15


Mass: 15410.694 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P19946

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)50S ribosomal protein uL16


Mass: 16223.049 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P14577

Cellular component

Molecular function

Biological process

#46: Polypeptide(L)50S ribosomal protein bL17


Mass: 13774.806 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P20277

Cellular component

Molecular function

Biological process

#47: Polypeptide(L)50S ribosomal protein uL18


Mass: 12993.829 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P46899

Cellular component

Molecular function

Biological process

#48: Polypeptide(L)50S ribosomal protein bL19


Mass: 13416.853 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: O31742

Cellular component

Molecular function

Biological process

#49: Polypeptide(L)50S ribosomal protein bL20


Mass: 13669.189 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P55873

Cellular component

Molecular function

Biological process

#50: Polypeptide(L)50S ribosomal protein bL21


Mass: 11296.081 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P26908

Cellular component

Molecular function

Biological process

#51: Polypeptide(L)50S ribosomal protein uL22


Mass: 12481.608 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42060

Cellular component

Molecular function

Biological process

#52: Polypeptide(L)50S ribosomal protein uL23


Mass: 10978.813 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42924

Cellular component

Molecular function

Biological process

#53: Polypeptide(L)50S ribosomal protein uL24


Mass: 11166.120 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P0CI78

Cellular component

Molecular function

Biological process

#54: Polypeptide(L)50S ribosomal protein bL27


Mass: 10391.855 Da / Num. of mol.: 1
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P05657

Cellular component

Molecular function

Biological process

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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

Component
IDNameTypeParent ID
1B. subtilis MifM-stalled ribosome complexRIBOSOME0
270S ribosomeRIBOSOME1
3Membrane protein insertion and folding monitor1
4tRNA-Asp1
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 2 nm pre-coated Quantifoil R3/3 holey carbon support grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Apr 12, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 125085 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: RECONSTRUCTION
CTF correctionDetails: defocus groups
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 305045 / Nominal pixel size: 1.108 / Actual pixel size: 1.108
Details: Since images from microscopy were processed in the absence of spatial frequencies higher than 8 A, a FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012). (Single particle--Applied symmetry: C1)
Symmetry type: POINT
Number of atoms included #LASTProtein: 35090 / Nucleic acid: 100335 / Ligand: 0 / Solvent: 0 / Total: 135425

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