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- PDB-8xz3: Mycobacterium smegmatis 50S ribosomal subunit with Erythromycin -

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Basic information

Entry
Database: PDB / ID: 8xz3
TitleMycobacterium smegmatis 50S ribosomal subunit with Erythromycin
Components
  • (50S ribosomal protein ...) x 5
  • (Large ribosomal subunit protein ...) x 27
  • 23S rRNA
  • 5S rRNA
KeywordsRIBOSOME / Antibiotic
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / metal ion 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 L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : ...: / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 1. / : / Ribosomal protein L10 / Ribosomal protein L10P / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / : / Ribosomal protein L16 / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24
Similarity search - Domain/homology
ERYTHROMYCIN A / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 ...ERYTHROMYCIN A / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Uncharacterized protein / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSrinivasan, K. / Banerjee, A. / Sengupta, J.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/001788 India
Science and Engineering Research Board (SERB)SPF/2021/000141 India
CitationJournal: Structure / Year: 2024
Title: Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria.
Authors: Krishnamoorthi Srinivasan / Aneek Banerjee / Jayati Sengupta /
Abstract: Mycobacterial HflX confers resistance against macrolide antibiotics. However, the exact molecular mechanism is poorly understood. To gain further insights, we determined the cryo-EM structures of M. ...Mycobacterial HflX confers resistance against macrolide antibiotics. However, the exact molecular mechanism is poorly understood. To gain further insights, we determined the cryo-EM structures of M. smegmatis (Msm) HflX-50S subunit and 50S subunit-erythromycin (ERY) complexes at a global resolution of approximately 3 Å. A conserved nucleotide A2286 at the gate of nascent peptide exit tunnel (NPET) adopts a swayed conformation in HflX-50S complex and interacts with a loop within the linker helical (LH) domain of MsmHflX that contains an additional 9 residues insertion. Interestingly, the swaying of this nucleotide, which is usually found in the non-swayed conformation, is induced by erythromycin binding. Furthermore, we observed that erythromycin decreases HflX's ribosome-dependent GTP hydrolysis, resulting in its enhanced binding and anti-association activity on the 50S subunit. Our findings reveal how mycobacterial HflX senses the presence of macrolides at the peptide tunnel entrance and confers antibiotic resistance in mycobacteria.
History
DepositionJan 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
3: 50S ribosomal protein bL37
A: 23S rRNA
B: 5S rRNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
H: 50S ribosomal protein L9
I: Large ribosomal subunit protein uL10
J: Large ribosomal subunit protein uL11
K: Large ribosomal subunit protein uL13
L: 50S ribosomal protein L14
M: Large ribosomal subunit protein uL15
N: Large ribosomal subunit protein uL16
O: Large ribosomal subunit protein bL17
P: Large ribosomal subunit protein uL18
Q: 50S ribosomal protein L19
R: Large ribosomal subunit protein bL20
S: Large ribosomal subunit protein bL21
T: Large ribosomal subunit protein uL22
U: Large ribosomal subunit protein uL23
V: Large ribosomal subunit protein uL24
W: Large ribosomal subunit protein bL25
X: Large ribosomal subunit protein bL27
Y: Large ribosomal subunit protein bL28
Z: Large ribosomal subunit protein uL29
a: Large ribosomal subunit protein uL30
b: Large ribosomal subunit protein bL32
c: Large ribosomal subunit protein bL33A
d: Large ribosomal subunit protein bL34
e: Large ribosomal subunit protein bL35
f: 50S ribosomal protein L36
g: Large ribosomal subunit protein bL31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,454,16135
Polymers1,453,42834
Non-polymers7341
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S ribosomal protein ... , 5 types, 5 molecules 3HLQf

#1: Protein/peptide 50S ribosomal protein bL37


Mass: 2710.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTP4
#9: Protein 50S ribosomal protein L9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7F6
#13: Protein 50S ribosomal protein L14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSF9
#18: Protein 50S ribosomal protein L19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QV42
#33: Protein/peptide 50S ribosomal protein L36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL4

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RNA chain , 2 types, 2 molecules AB

#2: RNA chain 23S rRNA


Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627
#3: RNA chain 5S rRNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: GenBank: 118168627

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Large ribosomal subunit protein ... , 27 types, 27 molecules CDEFGIJKMNOPRSTUVWXYZabcdeg

#4: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30008.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD4
#5: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 22621.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD1
#6: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22346.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD2
#7: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20588.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG1
#8: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19165.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG4
#10: Protein Large ribosomal subunit protein uL10 / 50S ribosomal protein L10


Mass: 13095.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS62
#11: Protein Large ribosomal subunit protein uL11 / 50S ribosomal protein L11


Mass: 14109.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS45
#12: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16015.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSP8
#14: Protein Large ribosomal subunit protein uL15


Mass: 15383.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G436
#15: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15498.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD8
#16: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 13210.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSL9
#17: Protein Large ribosomal subunit protein uL18


Mass: 13580.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FGD9
#19: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 14035.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU6
#20: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 10724.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R151
#21: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12408.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD6
#22: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10748.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD3
#23: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG0
#24: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 20331.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7GFB2
#25: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 8322.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R150
#26: Protein Large ribosomal subunit protein bL28


Mass: 6759.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7FJ52
#27: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7590.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSD9
#28: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6761.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QSG7
#29: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6050.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R3I9
#30: Protein/peptide Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 5833.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QS39
#31: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5391.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R7K0
#32: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7167.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYU7
#34: Protein/peptide Large ribosomal subunit protein bL31 / 50S ribosomal protein L31


Mass: 5257.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R215

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Non-polymers , 1 types, 1 molecules

#35: Chemical ChemComp-ERY / ERYTHROMYCIN A


Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H67NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM

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Details

Has ligand of interestY

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Mycobacterium smegmatis 50S ribosomal subunit-erythromycin complexCOMPLEXPurified Mycobacterium smegmatis 50S ribosomal subunit bound to erythromycin#1-#340MULTIPLE SOURCES
2Mycobacterium smegmatis 50S ribosomal subunitORGANELLE OR CELLULAR COMPONENT#1-#341NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mycolicibacterium smegmatis MC2 155 (bacteria)246196
32Mycolicibacterium smegmatis MC2 155 (bacteria)246196
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
22Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3300 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 28.75 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
9PHENIX1.20.1-4487model refinement
10RELION3.0.8initial Euler assignment
11RELION3.0.8final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43558 / Symmetry type: POINT

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