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- PDB-6dzk: Cryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosom... -

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Basic information

Entry
Database: PDB / ID: 6dzk
TitleCryo-EM Structure of Mycobacterium smegmatis C(minus) 30S ribosomal subunit with MPY
Components
  • (30S ribosomal protein ...) x 19
  • 16S rRNA
  • 50S ribosomal protein L31
  • Conserved domain proteinProtein domain
  • Ribosome hibernation promoting factor
KeywordsRIBOSOME / Hibernation factor complex
Function / homologyL28p-like / Ribosomal protein S3, C-terminal domain superfamily / 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 / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / RNA-binding S4 domain superfamily ...L28p-like / Ribosomal protein S3, C-terminal domain superfamily / 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 / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S18 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosome hibernation promotion factor-like / Ribosomal protein S20 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein S2 / Ribosomal protein S6 superfamily / Ribosomal protein S6 signature. / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S16 domain superfamily / Ribosomal protein S7 domain / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4/S9 / Ribosomal protein S19 conserved site / Ribosomal protein S15 / Ribosomal protein S5, N-terminal domain / Ribosomal protein S6, plastid/chloroplast / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein S13 signature. / Ribosomal protein S4 signature. / Ribosomal protein S5 signature. / Ribosomal protein S3 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. / Ribosomal protein S7 signature. / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein S10p/S20e / KH domain / Ribosomal protein S5, C-terminal domain / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein S20 / S4 domain / Ribosomal protein S6 / Ribosomal protein L31 / 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 S6, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S2 signature 1. / Ribosomal protein S3, C-terminal / K Homology domain / K Homology domain, type 2 / Ribosome hibernation promoting factor/RaiA / RNA-binding S4 domain / Ribosomal protein S20 / Ribosomal protein S19/S15 / Ribosomal protein L31 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S13 / Ribosomal protein S2 / Ribosomal protein S10 / Ribosomal protein S18 / Ribosomal protein S14 / Ribosomal protein S16, conserved site / Ribosomal protein S5 / 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 L31 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 S5, C-terminal
Function and homology information
Specimen sourceMycobacterium smegmatis str. MC2 155 (bacteria)
Mycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsSharma, M.R. / Li, Y. / Korripella, R. / Yang, Y. / Kaushal, P.S. / Lin, Q. / Wade, J.T. / Gray, A.G. / Derbyshire, K.M. / Agrawal, R.K. / Ojha, A.
Funding supportUnited States , 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteGM061576United States
National Institutes of Health/National Human Genome Research InstituteAI107595United States
National Institutes of Health/National Human Genome Research InstituteAI097191United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Zinc depletion induces ribosome hibernation in mycobacteria.
Authors: Yunlong Li / Manjuli R Sharma / Ravi K Koripella / Yong Yang / Prem S Kaushal / Qishan Lin / Joseph T Wade / Todd A Gray / Keith M Derbyshire / Rajendra K Agrawal / Anil K Ojha
Abstract: Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc ...Bacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome. MPY binding is dependent on another mycobacterial protein, MPY recruitment factor (MRF), which is induced on zinc depletion, and interacts with C- ribosomes. MPY binding confers structural stability to C- ribosomes, promoting survival of growth-arrested cells under zinc-limiting conditions. Binding of MPY also has direct influence on the dynamics of aminoglycoside-binding pockets of the C- ribosome to inhibit binding of these antibiotics. Together, our data suggest that zinc limitation leads to ribosome hibernation and aminoglycoside resistance in mycobacteria. Furthermore, our observation of the expression of the proteins of C- ribosomes in in a mouse model of infection suggests that ribosome hibernation could be relevant in our understanding of persistence and drug tolerance of the pathogen encountered during chemotherapy of TB.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 5, 2018 / Release: Sep 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 19, 2018Structure modelrepositoryInitial release
1.1Oct 24, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Assembly

Deposited unit
A: 16S rRNA
B: Conserved domain protein
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
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
V: 30S ribosomal protein S2
r: 30S ribosomal protein S18 1
Y: Ribosome hibernation promoting factor
N: 30S ribosomal protein S14
g: 50S ribosomal protein L31


Theoretical massNumber of molelcules
Total (without water)829,16423
Polyers829,16423
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA


Mass: 490111.719 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627

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Protein/peptide , 3 types, 3 molecules BYg

#2: Protein/peptide Conserved domain protein / Protein domain


Mass: 4033.104 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QR10*PLUS
#21: Protein/peptide Ribosome hibernation promoting factor / HPF


Mass: 26447.615 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTK6
#23: Protein/peptide 50S ribosomal protein L31 /


Mass: 9141.198 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R554

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

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


Mass: 30191.227 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD7
#4: Protein/peptide 30S ribosomal protein S4 /


Mass: 23415.787 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL7
#5: Protein/peptide 30S ribosomal protein S5 /


Mass: 21814.893 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG6
#6: Protein/peptide 30S ribosomal protein S6 /


Mass: 10991.637 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0A0D6J3X3
#7: Protein/peptide 30S ribosomal protein S7 /


Mass: 17660.375 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS97
#8: Protein/peptide 30S ribosomal protein S8 /


Mass: 14361.442 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSG3
#9: Protein/peptide 30S ribosomal protein S9 /


Mass: 16794.365 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSP9
#10: Protein/peptide 30S ribosomal protein S10 /


Mass: 11454.313 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD0
#11: Protein/peptide 30S ribosomal protein S11 /


Mass: 14671.762 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL6
#12: Protein/peptide 30S ribosomal protein S12 /


Mass: 13896.366 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS96
#13: Protein/peptide 30S ribosomal protein S13 /


Mass: 14249.619 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL5
#14: Protein/peptide 30S ribosomal protein S15 /


Mass: 10236.900 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVQ3
#15: Protein/peptide 30S ribosomal protein S16 /


Mass: 16795.207 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QV37
#16: Protein/peptide 30S ribosomal protein S17 /


Mass: 11127.002 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSE0
#17: Protein/peptide 30S ribosomal protein S19 /


Mass: 10800.602 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSD5
#18: Protein/peptide 30S ribosomal protein S20 /


Mass: 9556.104 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R102
#19: Protein/peptide 30S ribosomal protein S2 /


Mass: 30145.230 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QVB8
#20: Protein/peptide 30S ribosomal protein S18 1 / Ribosome


Mass: 9606.369 Da / Num. of mol.: 1 / Source: (natural) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R549
#22: Protein/peptide 30S ribosomal protein S14 /


Mass: 11661.530 Da / Num. of mol.: 1
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0R550

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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: Mycobacterium smegmatis (Cminus) 70S with MPY / Type: RIBOSOME
Details: Mycobacterium smegmatis 30S ribosomal subunit with MPY
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 67 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4RELION2.01CTF correction
10RELION2.01initial Euler assignment
12RELION2.01classificationRelion used for image processing and Refinement
13RELION2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 205510
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 66840 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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