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- PDB-9e1s: Cryo-EM structure of the ribosome-tunnel occluding hibernation fa... -

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Basic information

Entry
Database: PDB / ID: 9e1s
TitleCryo-EM structure of the ribosome-tunnel occluding hibernation factor bound to the Mycobacterium tuberculosis C- 50S ribosomal subunit
Components
  • (50S ribosomal protein ...) x 27
  • (Large ribosomal subunit protein ...) x 2
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosomal tunnel occlusion factor-RTOF
KeywordsRIBOSOME / hibernating ribosome / Mycobacterium tuberculosis / nascent peptide exit tunnel / 50S / hibernation factor / TRANSLATION
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / translation / structural constituent of ribosome / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L20 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L24 / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal protein L2 signature. / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L13 signature. / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / : / Ribosomal protein L10e/L16 / Ribosomal protein L13, conserved site
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL3 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21 / : / Large ribosomal subunit protein uL14
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsMajumdar, S. / Ojha, A.K. / Agrawal, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32422 United States
CitationJournal: Biorxiv / Year: 2024
Title: A Novel Actinobacteria-Specific Ribosome Hibernation Factor in Mycobacterium tuberculosis
Authors: Majumdar, S. / Li, Y. / Manjari, S.R. / Gamper, H.B. / Hou, Y.M. / Banavali, N.K. / Ojha, A.K. / Agrawal, R.K.
History
DepositionOct 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
7: 50S ribosomal protein bL37
I: 23S ribosomal RNA
1: Ribosomal tunnel occlusion factor-RTOF
0: 50S ribosomal protein L32
2: 50S ribosomal protein bL34
3: 50S ribosomal protein L35
4: 50S ribosomal protein bL36
B: 5S ribosomal RNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
J: 50S ribosomal protein L13
K: Large ribosomal subunit protein uL14
L: 50S ribosomal protein L15
M: 50S ribosomal protein L16
N: 50S ribosomal protein L17
O: 50S ribosomal protein L18
P: 50S ribosomal protein L19
Q: 50S ribosomal protein L20
R: Large ribosomal subunit protein bL21
S: 50S ribosomal protein L22
T: 50S ribosomal protein L23
V: 50S ribosomal protein L25
W: 50S ribosomal protein L27
Y: 50S ribosomal protein L29
Z: 50S ribosomal protein L30
b: 50S ribosomal protein bL33-c minus
y: 50S ribosomal protein bL28-c minus
U: 50S ribosomal protein uL24


Theoretical massNumber of molelcules
Total (without water)1,466,70232
Polymers1,466,70232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 27 types, 27 molecules 70234CDEFGHJLMNOPQSTVWYZbyU

#1: Protein/peptide 50S ribosomal protein bL37


Mass: 2882.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0AB73YSK1
#4: Protein 50S ribosomal protein L32


Mass: 6525.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IMI5
#5: Protein/peptide 50S ribosomal protein bL34


Mass: 5643.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
#6: Protein 50S ribosomal protein L35


Mass: 7241.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KKY9
#7: Protein/peptide 50S ribosomal protein bL36


Mass: 4323.239 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
#9: Protein 50S ribosomal protein L2


Mass: 30644.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H5T7
#10: Protein 50S ribosomal protein L3


Mass: 23127.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HU18
#11: Protein 50S ribosomal protein L4


Mass: 23779.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9H1
#12: Protein 50S ribosomal protein L5


Mass: 21052.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045HUU0
#13: Protein 50S ribosomal protein L6


Mass: 19408.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JJU1
#14: Protein 50S ribosomal protein L9


Mass: 16196.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JW48
#15: Protein 50S ribosomal protein L13


Mass: 21646.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A0T9D5H2
#17: Protein 50S ribosomal protein L15


Mass: 15566.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWY0
#18: Protein 50S ribosomal protein L16


Mass: 15724.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IWV9
#19: Protein 50S ribosomal protein L17


Mass: 19512.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IVA2
#20: Protein 50S ribosomal protein L18


Mass: 13211.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JK28
#21: Protein 50S ribosomal protein L19


Mass: 13041.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IDD2
#22: Protein 50S ribosomal protein L20


Mass: 14557.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045KJ85
#24: Protein 50S ribosomal protein L22


Mass: 20424.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H760
#25: Protein 50S ribosomal protein L23


Mass: 10976.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045J9M3
#26: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 22466.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045JAK4
#27: Protein 50S ribosomal protein L27


Mass: 8987.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045K0G1
#28: Protein 50S ribosomal protein L29


Mass: 8872.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IQ64
#29: Protein 50S ribosomal protein L30


Mass: 7361.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045H4J2
#30: Protein 50S ribosomal protein bL33-c minus


Mass: 6604.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
#31: Protein 50S ribosomal protein bL28-c minus


Mass: 9099.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
#32: Protein 50S ribosomal protein uL24 / 50S ribosomal protein L24


Mass: 11500.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A045IXU4

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RNA chain , 2 types, 2 molecules IB

#2: RNA chain 23S ribosomal RNA


Mass: 1017792.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 984989958
#8: RNA chain 5S ribosomal RNA


Mass: 37097.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: GenBank: 1251771551

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Protein , 1 types, 1 molecules 1

#3: Protein Ribosomal tunnel occlusion factor-RTOF


Mass: 6810.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)

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Large ribosomal subunit protein ... , 2 types, 2 molecules KR

#16: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13451.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: P66070
#23: Protein Large ribosomal subunit protein bL21


Mass: 11173.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria) / References: UniProt: A0A2I7W9M4

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mycobacterium tuberculosis C- 50S ribosomal subunit bound to the ribosomal tunnel occlusion factor-RTOF
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Buffer solutionpH: 7.5 / Details: Polymix buffer
Buffer component
IDConc.NameFormulaBuffer-ID
195 mMPotassium chlorideKCl1
25 mMAmmonium chlorideNH4Cl1
35 mMMagnesium acetateMg(OAC)21
40.5 mMCalcium chlorideCaCl21
58 mMPutrescine1
61 mMSpermidine1
75 mMPotassium phosphateKP1
81 mMDithiothreitol1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 0.001 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.75 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13499

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4.0particle selection
2Leginonimage acquisition
4cryoSPARCv4.4.0CTF correction
10cryoSPARCv4.4.0final Euler assignment
11cryoSPARCv4.4.0classification
12cryoSPARCv4.4.03D reconstruction
13PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5471811
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 257214 / Symmetry type: POINT
Atomic model buildingB value: 60.5 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 7MT7

7mt7


Accession code: 7MT7 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007103747
ELECTRON MICROSCOPYf_angle_d0.831156233
ELECTRON MICROSCOPYf_dihedral_angle_d15.10642522
ELECTRON MICROSCOPYf_chiral_restr0.04820062
ELECTRON MICROSCOPYf_plane_restr0.0087810

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