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- PDB-9cn3: Human 39S mitoribosome in complex with antibiotic Linezolid -

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Basic information

Entry
Database: PDB / ID: 9cn3
TitleHuman 39S mitoribosome in complex with antibiotic Linezolid
Components
  • (39S ribosomal protein ...) x 46
  • 16S rRNA
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • Mitochondrial ribosomal protein L18, isoform CRA_b
  • P-site finger
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein 63, mitochondrial
  • cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA
  • tRNA
KeywordsRIBOSOME/ANTIBIOTIC / Mitochondrial ribosome / Oxazolidinone / antibiotics / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase ...mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / mitochondrial translation / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / fibrillar center / cell junction / double-stranded RNA binding / large ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / mitochondrial inner membrane / negative regulation of translation / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / positive regulation of DNA-templated transcription / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial ...: / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L37, mitochondrial / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L28 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L35, mitochondrial / Ribosomal protein L51, mitochondrial / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Ribosomal protein L37/S30 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / : / : / Mitochondrial 28S ribosomal protein S30 (PDCD9) / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / MRPL44, double-stranded RNA binding domain / : / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / : / Large ribosomal subunit protein bL9m C-terminal domain / Large ribosomal subunit protein bL9m N-terminal domain / Tim44-like domain / Tim44-like domain / Tim44 / : / : / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L27/L41, mitochondrial / : / Mitochondrial ribosomal protein L27 / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / : / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Beta-grasp domain superfamily / NTF2-like domain superfamily / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / 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/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily
Similarity search - Domain/homology
Chem-ZLD / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL22m ...Chem-ZLD / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL12m / Large ribosomal subunit protein bL28m / Large ribosomal subunit protein mL49 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein uL23m / Large ribosomal subunit protein mL51 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein mL54 / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein bL21m / Large ribosomal subunit protein mL55 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL41 / Large ribosomal subunit protein mL50 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL64 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein mL53 / Large ribosomal subunit protein mL48 / Large ribosomal subunit protein bL34m / Large ribosomal subunit protein mL63 / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein bL20m / Large ribosomal subunit protein uL13m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein mL37 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL65 / Large ribosomal subunit protein mL40 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein mL66 / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / Large ribosomal subunit protein bL36m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL42
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsRaskar, T. / Bibel, B. / Galonic Fujimori, D. / Fraser, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI137270 United States
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics.
Authors: Brianna Bibel / Tushar Raskar / Mary Couvillion / Muhoon Lee / Jordan I Kleinman / Nono Takeuchi-Tomita / L Stirling Churchman / James S Fraser / Danica Galonić Fujimori /
Abstract: The antibiotics chloramphenicol (CHL) and oxazolidinones, including linezolid (LZD), are known to inhibit mitochondrial translation. This can result in serious, potentially deadly, side effects when ...The antibiotics chloramphenicol (CHL) and oxazolidinones, including linezolid (LZD), are known to inhibit mitochondrial translation. This can result in serious, potentially deadly, side effects when used therapeutically. Although the mechanism by which CHL and LZD inhibit bacterial ribosomes has been elucidated in detail, their mechanism of action against mitochondrial ribosomes has yet to be explored. CHL and oxazolidinones bind to the ribosomal peptidyl transfer center (PTC) of the bacterial ribosome and prevent incorporation of incoming amino acids under specific sequence contexts, causing ribosomes to stall only at certain sequences. Through mitoribosome profiling, we show that inhibition of mitochondrial ribosomes is similarly context-specific-CHL and LZD lead to mitoribosome stalling primarily when there is an alanine, serine, or threonine in the penultimate position of the nascent peptide chain. We further validate context-specific stalling through in vitro translation assays. A high-resolution cryo-electron microscopy structure of LZD bound to the PTC of the human mitoribosome shows extensive similarity to the mode of bacterial inhibition and also suggests potential avenues for altering selectivity. Our findings could help inform the rational development of future, less mitotoxic, antibiotics, which are critically needed in the current era of increasing antimicrobial resistance.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: 39S ribosomal protein L32, mitochondrial
1: 39S ribosomal protein L33, mitochondrial
2: 39S ribosomal protein L34, mitochondrial
3: 39S ribosomal protein L35, mitochondrial
4: 39S ribosomal protein L36, mitochondrial
5: 39S ribosomal protein L37, mitochondrial
6: 39S ribosomal protein L38, mitochondrial
7: 39S ribosomal protein L39, mitochondrial
8: 39S ribosomal protein L40, mitochondrial
9: 39S ribosomal protein L41, mitochondrial
A: 16S rRNA
B: tRNA
D: 39S ribosomal protein L2, mitochondrial
E: 39S ribosomal protein L3, mitochondrial
F: 39S ribosomal protein L4, mitochondrial
H: 39S ribosomal protein L9, mitochondrial
I: 39S ribosomal protein L10, mitochondrial
J: 39S ribosomal protein L11, mitochondrial
K: 39S ribosomal protein L13, mitochondrial
L: 39S ribosomal protein L14, mitochondrial
M: 39S ribosomal protein L15, mitochondrial
N: 39S ribosomal protein L16, mitochondrial
O: 39S ribosomal protein L17, mitochondrial
P: Mitochondrial ribosomal protein L18, isoform CRA_b
Q: 39S ribosomal protein L19, mitochondrial
R: 39S ribosomal protein L20, mitochondrial
S: 39S ribosomal protein L21, mitochondrial
T: 39S ribosomal protein L22, mitochondrial
U: 39S ribosomal protein L23, mitochondrial
V: 39S ribosomal protein L24, mitochondrial
W: 39S ribosomal protein L27, mitochondrial
X: 39S ribosomal protein L28, mitochondrial
Y: 39S ribosomal protein L47, mitochondrial
Z: 39S ribosomal protein L30, mitochondrial
a: 39S ribosomal protein L42, mitochondrial
b: 39S ribosomal protein L43, mitochondrial
c: 39S ribosomal protein L44, mitochondrial
d: 39S ribosomal protein L45, mitochondrial
e: 39S ribosomal protein L46, mitochondrial
f: 39S ribosomal protein L48, mitochondrial
g: 39S ribosomal protein L49, mitochondrial
h: 39S ribosomal protein L50, mitochondrial
i: 39S ribosomal protein L51, mitochondrial
j: cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA
k: 39S ribosomal protein L53, mitochondrial
l: 39S ribosomal protein L54, mitochondrial
m: 39S ribosomal protein L55, mitochondrial
o: Ribosomal protein 63, mitochondrial
p: Peptidyl-tRNA hydrolase ICT1, mitochondrial
q: Growth arrest and DNA damage-inducible proteins-interacting protein 1
r: 39S ribosomal protein S18a, mitochondrial
s: 39S ribosomal protein S30, mitochondrial
u: P-site finger
TA: 39S ribosomal protein L12, mitochondrial
TB: 39S ribosomal protein L12, mitochondrial
TC: 39S ribosomal protein L12, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,861,058162
Polymers1,858,04656
Non-polymers3,013106
Water74,3844129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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39S ribosomal protein ... , 46 types, 48 molecules 0123456789DEFHIJKLMNOQRSTUVWXY...

#1: Protein 39S ribosomal protein L32, mitochondrial / MRP-L32 / Mitochondrial large ribosomal subunit protein bL32m


Mass: 21437.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC8
#2: Protein 39S ribosomal protein L33, mitochondrial / MRP-L33 / Mitochondrial large ribosomal subunit protein bL33m


Mass: 7635.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75394
#3: Protein 39S ribosomal protein L34, mitochondrial / MRP-L34 / Mitochondrial large ribosomal subunit protein bL34m


Mass: 10183.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQ48
#4: Protein 39S ribosomal protein L35, mitochondrial / MRP-L35 / Mitochondrial large ribosomal subunit protein bL35m


Mass: 21558.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZE8
#5: Protein 39S ribosomal protein L36, mitochondrial / MRP-L36 / BRCA1-interacting protein 1 / Mitochondrial large ribosomal subunit protein bL36m


Mass: 11809.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J6
#6: Protein 39S ribosomal protein L37, mitochondrial / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit ...MRP-L37 / 39S ribosomal protein L2 / mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit protein mL37


Mass: 48183.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE1
#7: Protein 39S ribosomal protein L38, mitochondrial / MRP-L38 / Mitochondrial large ribosomal subunit protein mL38


Mass: 44659.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DV4
#8: Protein 39S ribosomal protein L39, mitochondrial / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / MRP-L5 / Mitochondrial large ribosomal subunit ...MRP-L39 / 39S ribosomal protein L5 / mitochondrial / MRP-L5 / Mitochondrial large ribosomal subunit protein mL39


Mass: 38764.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYK5
#9: Protein 39S ribosomal protein L40, mitochondrial / MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal- ...MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal-containing protein deleted in velocardiofacial syndrome / Up-regulated in metastasis


Mass: 24534.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NQ50
#10: Protein 39S ribosomal protein L41, mitochondrial / MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal protein L41 ...MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal protein L41 / Cell proliferation-inducing gene 3 protein / MRP-L27 homolog / Mitochondrial large ribosomal subunit protein mL41


Mass: 15404.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IXM3
#13: Protein 39S ribosomal protein L2, mitochondrial / MRP-L2 / Mitochondrial large ribosomal subunit protein uL2m


Mass: 33355.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653
#14: Protein 39S ribosomal protein L3, mitochondrial / MRP-L3 / Mitochondrial large ribosomal subunit protein uL3m


Mass: 38689.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09001
#15: Protein 39S ribosomal protein L4, mitochondrial / MRP-L4 / Mitochondrial large ribosomal subunit protein uL4m


Mass: 34970.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#16: Protein 39S ribosomal protein L9, mitochondrial / MRP-L9 / Mitochondrial large ribosomal subunit protein bL9m


Mass: 30296.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#17: Protein 39S ribosomal protein L10, mitochondrial / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / MRP-L8 / Mitochondrial large ribosomal subunit ...MRP-L10 / 39S ribosomal protein L8 / mitochondrial / MRP-L8 / Mitochondrial large ribosomal subunit protein uL10m


Mass: 29322.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7H8
#18: Protein 39S ribosomal protein L11, mitochondrial / MRP-L11 / Mitochondrial large ribosomal subunit protein uL11m


Mass: 20716.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B7
#19: Protein 39S ribosomal protein L13, mitochondrial / MRP-L13 / Mitochondrial large ribosomal subunit protein uL13m


Mass: 20722.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#20: Protein 39S ribosomal protein L14, mitochondrial / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / MRP-L32 / Mitochondrial large ribosomal ...MRP-L14 / 39S ribosomal protein L32 / mitochondrial / MRP-L32 / Mitochondrial large ribosomal subunit protein uL14m


Mass: 15973.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1L8
#21: Protein 39S ribosomal protein L15, mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein uL15m


Mass: 33473.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P015
#22: Protein 39S ribosomal protein L16, mitochondrial / MRP-L16 / Mitochondrial large ribosomal subunit protein uL16m


Mass: 28496.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#23: Protein 39S ribosomal protein L17, mitochondrial / MRP-L17 / LYST-interacting protein 2 / Mitochondrial large ribosomal subunit protein bL17m


Mass: 20083.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2
#25: Protein 39S ribosomal protein L19, mitochondrial / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal ...MRP-L19 / 39S ribosomal protein L15 / mitochondrial / MRP-L15 / Mitochondrial large ribosomal subunit protein bL19m


Mass: 33584.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49406
#26: Protein 39S ribosomal protein L20, mitochondrial / MRP-L20 / Mitochondrial large ribosomal subunit protein bL20m


Mass: 17479.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC9
#27: Protein 39S ribosomal protein L21, mitochondrial / MRP-L21 / Mitochondrial large ribosomal subunit protein bL21m


Mass: 22847.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z2W9
#28: Protein 39S ribosomal protein L22, mitochondrial


Mass: 24369.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: E7ESL0
#29: Protein 39S ribosomal protein L23, mitochondrial / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / ...MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / Ribosomal protein L23-like


Mass: 17807.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16540
#30: Protein 39S ribosomal protein L24, mitochondrial / MRP-L24 / Mitochondrial large ribosomal subunit protein uL24m


Mass: 24953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35
#31: Protein 39S ribosomal protein L27, mitochondrial / MRP-L27 / Mitochondrial large ribosomal subunit protein bL27m


Mass: 16102.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#32: Protein 39S ribosomal protein L28, mitochondrial / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / ...MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / Mitochondrial large ribosomal subunit protein bL28m


Mass: 30202.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#33: Protein 39S ribosomal protein L47, mitochondrial / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis- ...MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma metastasis-related protein 1


Mass: 29508.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HD33
#34: Protein 39S ribosomal protein L30, mitochondrial / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / MRP-L28 / Mitochondrial large ribosomal ...MRP-L30 / 39S ribosomal protein L28 / mitochondrial / MRP-L28 / Mitochondrial large ribosomal subunit protein uL30m


Mass: 18582.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TCC3
#35: Protein 39S ribosomal protein L42, mitochondrial / MRP-L42 / 39S ribosomal protein L31 / mitochondrial / MRP-L31 / Mitochondrial large ribosomal ...MRP-L42 / 39S ribosomal protein L31 / mitochondrial / MRP-L31 / Mitochondrial large ribosomal subunit protein mL42


Mass: 16691.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6G3
#36: Protein 39S ribosomal protein L43, mitochondrial / MRP-L43 / Mitochondrial large ribosomal subunit protein mL43 / Mitochondrial ribosomal protein bMRP36a


Mass: 17452.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983
#37: Protein 39S ribosomal protein L44, mitochondrial / MRP-L44 / Mitochondrial large ribosomal subunit protein mL44


Mass: 37583.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9H9J2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#38: Protein 39S ribosomal protein L45, mitochondrial / MRP-L45 / Mitochondrial large ribosomal subunit protein mL45


Mass: 35402.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRJ2
#39: Protein 39S ribosomal protein L46, mitochondrial / MRP-L46 / Mitochondrial large ribosomal subunit protein mL46 / P2ECSL


Mass: 31748.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H2W6
#40: Protein 39S ribosomal protein L48, mitochondrial / MRP-L48 / Mitochondrial large ribosomal subunit protein mL48


Mass: 21856.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96GC5
#41: Protein 39S ribosomal protein L49, mitochondrial / MRP-L49 / Mitochondrial large ribosomal subunit protein mL49 / Neighbor of FAU / NOF / Protein NOF1


Mass: 19225.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13405
#42: Protein 39S ribosomal protein L50, mitochondrial / MRP-L50 / Mitochondrial large ribosomal subunit protein mL50


Mass: 18349.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N5N7
#43: Protein 39S ribosomal protein L51, mitochondrial / MRP-L51 / Mitochondrial large ribosomal subunit protein mL51 / bMRP-64 / bMRP64


Mass: 15125.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q4U2R6
#45: Protein 39S ribosomal protein L53, mitochondrial / MRP-L53 / Mitochondrial large ribosomal subunit protein mL53


Mass: 12125.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL3
#46: Protein 39S ribosomal protein L54, mitochondrial / MRP-L54 / Mitochondrial large ribosomal subunit protein mL54


Mass: 15844.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P161
#47: Protein 39S ribosomal protein L55, mitochondrial / MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal ...MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ribosomal subunit protein mL55


Mass: 15160.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7F7
#51: Protein 39S ribosomal protein S18a, mitochondrial / S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal ...S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / Mitochondrial large ribosomal subunit protein bS18a / Mitochondrial large ribosomal subunit protein mL66


Mass: 22224.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVS2
#52: Protein 39S ribosomal protein S30, mitochondrial / S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit ...S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ribosomal subunit protein mS30 / Programmed cell death protein 9


Mass: 50429.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NP92
#54: Protein 39S ribosomal protein L12, mitochondrial / MRP-L12 / 5c5-2 / Mitochondrial large ribosomal subunit protein bL12m


Mass: 21378.164 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52815

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RNA chain , 2 types, 2 molecules AB

#11: RNA chain 16S rRNA


Mass: 500019.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1563835895
#12: RNA chain tRNA


Mass: 22961.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1896813692

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Protein , 6 types, 6 molecules Pjopqu

#24: Protein Mitochondrial ribosomal protein L18, isoform CRA_b / cDNA FLJ76688 / highly similar to Homo sapiens HSPC071 mRNA


Mass: 20465.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8K9D2
#44: Protein cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA


Mass: 13696.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8K7J6
#48: Protein Ribosomal protein 63, mitochondrial / hMRP63 / Mitochondrial large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / ...hMRP63 / Mitochondrial large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57


Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6
#49: Protein Peptidyl-tRNA hydrolase ICT1, mitochondrial / 39S ribosomal protein L58 / mitochondrial / MRP-L58 / Digestion substraction 1 / DS-1 / Immature ...39S ribosomal protein L58 / mitochondrial / MRP-L58 / Digestion substraction 1 / DS-1 / Immature colon carcinoma transcript 1 protein / Mitochondrial large ribosomal subunit protein mL62


Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase
#50: Protein Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6- ...39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6-interacting factor 1 / CRIF1 / Mitochondrial large ribosomal subunit protein mL64 / Papillomavirus L2-interacting nuclear protein 1 / PLINP-1 / p53-responsive gene 6 protein


Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8
#53: Protein P-site finger


Mass: 60442.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 4 types, 4235 molecules

#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 102 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-ZLD / N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide / Linezolid


Mass: 337.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20FN3O4
#58: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4129 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 39S subunit of human mitochondrial ribosome in complex with Linezolid
Type: RIBOSOME / Details: Purified from freestyle 293 cells / Entity ID: #1-#54 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 21 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: phenix.real_space_refine / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 347872 / Symmetry type: POINT

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