[English] 日本語
Yorodumi
- PDB-8k2b: Cryo-EM structure of the human 39S mitoribosome with Tigecycline -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k2b
TitleCryo-EM structure of the human 39S mitoribosome with Tigecycline
Components
  • (39S ribosomal protein ...) x 2
  • (Large ribosomal subunit protein ...) x 47
  • (Mitochondrial ...) x 3
  • 16s rRNA
  • Acyl carrier protein, mitochondrial
  • Val tRNA
KeywordsRIBOSOME / 39S mitoribosome / Tigecycline / antibiotic
Function / homology
Function and homology information


negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / protein lipoylation / negative regulation of ribosome biogenesis / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / Respiratory electron transport / mitochondrial translational termination ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / protein lipoylation / negative regulation of ribosome biogenesis / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / positive regulation of mitochondrial translation / Respiratory electron transport / mitochondrial translational termination / mitochondrial translational elongation / Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / translation release factor activity / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / mitochondrial large ribosomal subunit binding / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase activity / mitochondrial translation / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / acyl binding / acyl carrier activity / ribosomal large subunit binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / aerobic respiration / cellular response to leukemia inhibitory factor / fatty acid binding / ribosomal large subunit biogenesis / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / cell junction / large ribosomal subunit / double-stranded RNA binding / 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 / calcium ion binding / nucleolus / structural molecule activity / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial ...MIEF1-MP, LYR domain / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / : / 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 / : / : / Mitochondrial ribosomal protein L46 NUDIX / 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 / 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 / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / : / 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 / Acyl carrier protein (ACP) / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Phosphopantetheine attachment site / 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
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / TIGECYCLINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL22m / Mitochondrial ribosome and complex I assembly factor AltMIEF1 ...4'-PHOSPHOPANTETHEINE / TIGECYCLINE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL22m / Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Large ribosomal subunit protein bL33m / Large ribosomal subunit protein uL3m / Large ribosomal subunit protein bL19m / 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 / Mitochondrial assembly of ribosomal large subunit protein 1 / 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: 3.4 Å
AuthorsLi, X. / Wang, M. / Cheng, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
Authors: Xiang Li / Mengjiao Wang / Timo Denk / Robert Buschauer / Yi Li / Roland Beckmann / Jingdong Cheng /
Abstract: Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, ...Tigecycline is widely used for treating complicated bacterial infections for which there are no effective drugs. It inhibits bacterial protein translation by blocking the ribosomal A-site. However, even though it is also cytotoxic for human cells, the molecular mechanism of its inhibition remains unclear. Here, we present cryo-EM structures of tigecycline-bound human mitochondrial 55S, 39S, cytoplasmic 80S and yeast cytoplasmic 80S ribosomes. We find that at clinically relevant concentrations, tigecycline effectively targets human 55S mitoribosomes, potentially, by hindering A-site tRNA accommodation and by blocking the peptidyl transfer center. In contrast, tigecycline does not bind to human 80S ribosomes under physiological concentrations. However, at high tigecycline concentrations, in addition to blocking the A-site, both human and yeast 80S ribosomes bind tigecycline at another conserved binding site restricting the movement of the L1 stalk. In conclusion, the observed distinct binding properties of tigecycline may guide new pathways for drug design and therapy.
History
DepositionJul 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L1: 16s rRNA
L2: Val tRNA
LB: Large ribosomal subunit protein uL2m
LC: Large ribosomal subunit protein uL3m
LD: Large ribosomal subunit protein uL4m
LI: Large ribosomal subunit protein bL9m
LJ: Large ribosomal subunit protein uL10m
LK: Large ribosomal subunit protein uL11m
LM: Large ribosomal subunit protein uL13m
LN: Large ribosomal subunit protein uL14m
LO: Large ribosomal subunit protein uL15m
LP: Large ribosomal subunit protein uL16m
LQ: Large ribosomal subunit protein bL17m
LR: Mitochondrial ribosomal protein L18, isoform CRA_b
LS: Large ribosomal subunit protein bL19m
LT: Large ribosomal subunit protein bL20m
LU: Large ribosomal subunit protein bL21m
LV: 39S ribosomal protein L22, mitochondrial
LW: Large ribosomal subunit protein uL23m
LX: Large ribosomal subunit protein uL24m
La: Large ribosomal subunit protein bL27m
Lb: Large ribosomal subunit protein bL28m
Lu: Large ribosomal subunit protein uL29m
Ld: Large ribosomal subunit protein uL30m
Lf: Large ribosomal subunit protein bL32m
Lg: Large ribosomal subunit protein bL33m
Lh: Large ribosomal subunit protein bL34m
Li: Large ribosomal subunit protein bL35m
Lj: Large ribosomal subunit protein bL36m
Lk: Large ribosomal subunit protein mL37
Ll: Large ribosomal subunit protein mL38
Lm: Large ribosomal subunit protein mL39
Ln: Large ribosomal subunit protein mL40
Lo: Large ribosomal subunit protein mL41
Lp: Large ribosomal subunit protein mL42
Lq: Large ribosomal subunit protein mL43
Lr: Large ribosomal subunit protein mL44
Ls: Large ribosomal subunit protein mL45
Lt: Large ribosomal subunit protein mL46
Lv: Large ribosomal subunit protein mL48
Lw: Large ribosomal subunit protein mL49
Lx: Large ribosomal subunit protein mL50
Ly: Large ribosomal subunit protein mL51
Lz: 39S ribosomal protein L52, mitochondrial
L3: Large ribosomal subunit protein mL53
L4: Large ribosomal subunit protein mL54
L5: Large ribosomal subunit protein mL55
L6: Large ribosomal subunit protein mL63
L7: Large ribosomal subunit protein mL62
L8: Large ribosomal subunit protein mL64
SR: Large ribosomal subunit protein mL66
Sf: Large ribosomal subunit protein mL65
u: Mitochondrial assembly of ribosomal large subunit protein 1
v: Mitochondrial ribosome and complex I assembly factor AltMIEF1
w: Acyl carrier protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,796,198155
Polymers1,792,74755
Non-polymers3,451100
Water00
1


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

-
Components

-
RNA chain , 2 types, 2 molecules L1L2

#1: RNA chain 16s rRNA


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


Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

+
Large ribosomal subunit protein ... , 47 types, 47 molecules LBLCLDLILJLKLMLNLOLPLQLSLTLULWLXLaLbLuLdLfLgLhLiLjLkLlLmLnLo...

#3: Protein Large ribosomal subunit protein uL2m / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2


Mass: 33355.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T653
#4: Protein Large ribosomal subunit protein uL3m / 39S ribosomal protein L3 / mitochondrial / L3mt / MRP-L3


Mass: 38689.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09001
#5: Protein Large ribosomal subunit protein uL4m / 39S ribosomal protein L4 / mitochondrial / L4mt / MRP-L4


Mass: 34970.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD3
#6: Protein Large ribosomal subunit protein bL9m / 39S ribosomal protein L9 / mitochondrial / L9mt / MRP-L9


Mass: 30296.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#7: Protein Large ribosomal subunit protein uL10m / 39S ribosomal protein L10 / mitochondrial / L10mt / MRP-L10 / 39S ribosomal protein L8 / L8mt / MRP-L8


Mass: 29322.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7H8
#8: Protein Large ribosomal subunit protein uL11m / 39S ribosomal protein L11 / mitochondrial / L11mt / MRP-L11


Mass: 20716.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B7
#9: Protein Large ribosomal subunit protein uL13m / 39S ribosomal protein L13 / mitochondrial / L13mt / MRP-L13


Mass: 20722.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#10: Protein Large ribosomal subunit protein uL14m / 39S ribosomal protein L14 / mitochondrial / L14mt / MRP-L14 / 39S ribosomal protein L32 / L32mt / MRP-L32


Mass: 15973.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P1L8
#11: Protein Large ribosomal subunit protein uL15m / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15


Mass: 33473.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P015
#12: Protein Large ribosomal subunit protein uL16m / 39S ribosomal protein L16 / mitochondrial / L16mt / MRP-L16


Mass: 28496.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX20
#13: Protein Large ribosomal subunit protein bL17m / 39S ribosomal protein L17 / mitochondrial / L17mt / MRP-L17 / LYST-interacting protein 2


Mass: 20083.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX2
#15: Protein Large ribosomal subunit protein bL19m / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15 / 39S ribosomal protein L19 / L19mt / MRP-L19


Mass: 33584.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49406
#16: Protein Large ribosomal subunit protein bL20m / 39S ribosomal protein L20 / mitochondrial / L20mt / MRP-L20


Mass: 17479.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC9
#17: Protein Large ribosomal subunit protein bL21m / 39S ribosomal protein L21 / mitochondrial / L21mt / MRP-L21


Mass: 22847.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z2W9
#19: Protein Large ribosomal subunit protein uL23m / 39S ribosomal protein L23 / mitochondrial / L23mt / MRP-L23 / L23 mitochondrial-related protein / ...39S ribosomal protein L23 / mitochondrial / L23mt / MRP-L23 / L23 mitochondrial-related protein / 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
#20: Protein Large ribosomal subunit protein uL24m / 39S ribosomal protein L24 / mitochondrial / L24mt / MRP-L24


Mass: 24953.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96A35
#21: Protein Large ribosomal subunit protein bL27m / 39S ribosomal protein L27 / mitochondrial / L27mt / MRP-L27


Mass: 16102.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0M9
#22: Protein Large ribosomal subunit protein bL28m / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / Melanoma antigen p15 / Melanoma- ...39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes


Mass: 30202.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#23: Protein Large ribosomal subunit protein uL29m / 39S ribosomal protein L47 / mitochondrial / L47mt / MRP-L47 / Nasopharyngeal carcinoma metastasis- ...39S ribosomal protein L47 / mitochondrial / L47mt / MRP-L47 / 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
#24: Protein Large ribosomal subunit protein uL30m / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / 39S ribosomal protein L30 / L30mt / MRP-L30


Mass: 18582.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TCC3
#25: Protein Large ribosomal subunit protein bL32m / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32


Mass: 21437.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYC8
#26: Protein Large ribosomal subunit protein bL33m / 39S ribosomal protein L33 / mitochondrial / L33mt / MRP-L33


Mass: 7635.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75394
#27: Protein Large ribosomal subunit protein bL34m / 39S ribosomal protein L34 / mitochondrial / L34mt / MRP-L34


Mass: 10183.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQ48
#28: Protein Large ribosomal subunit protein bL35m / 39S ribosomal protein L35 / mitochondrial / L35mt / MRP-L35


Mass: 21558.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZE8
#29: Protein Large ribosomal subunit protein bL36m / 39S ribosomal protein L36 / mitochondrial / L36mt / MRP-L36 / BRCA1-interacting protein 1


Mass: 11809.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P0J6
#30: Protein Large ribosomal subunit protein mL37 / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2 / 39S ribosomal protein L37 / L37mt / MRP-L37


Mass: 48183.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE1
#31: Protein Large ribosomal subunit protein mL38 / 39S ribosomal protein L38 / mitochondrial / L38mt / MRP-L38


Mass: 44659.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DV4
#32: Protein Large ribosomal subunit protein mL39 / 39S ribosomal protein L39 / mitochondrial / L39mt / MRP-L39 / 39S ribosomal protein L5 / L5mt / MRP-L5


Mass: 38764.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NYK5
#33: Protein Large ribosomal subunit protein mL40 / 39S ribosomal protein L40 / mitochondrial / L40mt / MRP-L40 / Nuclear localization signal- ...39S ribosomal protein L40 / mitochondrial / L40mt / MRP-L40 / 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
#34: Protein Large ribosomal subunit protein mL41 / 39S ribosomal protein L41 / mitochondrial / L41mt / MRP-L41 / Bcl-2-interacting mitochondrial ...39S ribosomal protein L41 / mitochondrial / L41mt / MRP-L41 / Bcl-2-interacting mitochondrial ribosomal protein L41 / Cell proliferation-inducing gene 3 protein / MRP-L27 homolog


Mass: 15404.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IXM3
#35: Protein Large ribosomal subunit protein mL42 / 39S ribosomal protein L31 / mitochondrial / L31mt / MRP-L31 / 39S ribosomal protein L42 / L42mt / MRP-L42


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 Large ribosomal subunit protein mL43 / 39S ribosomal protein L43 / mitochondrial / L43mt / MRP-L43 / Mitochondrial ribosomal protein bMRP36a


Mass: 23457.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983
#37: Protein Large ribosomal subunit protein mL44 / 39S ribosomal protein L44 / mitochondrial / L44mt / MRP-L44


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 Large ribosomal subunit protein mL45 / 39S ribosomal protein L45 / mitochondrial / L45mt / MRP-L45


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 Large ribosomal subunit protein mL46 / 39S ribosomal protein L46 / mitochondrial / L46mt / MRP-L46 / 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 Large ribosomal subunit protein mL48 / 39S ribosomal protein L48 / mitochondrial / L48mt / MRP-L48


Mass: 23970.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96GC5
#41: Protein Large ribosomal subunit protein mL49 / 39S ribosomal protein L49 / mitochondrial / L49mt / MRP-L49 / 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 Large ribosomal subunit protein mL50 / 39S ribosomal protein L50 / mitochondrial / L50mt / MRP-L50


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 Large ribosomal subunit protein mL51 / 39S ribosomal protein L51 / mitochondrial / L51mt / MRP-L51 / 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 Large ribosomal subunit protein mL53 / 39S ribosomal protein L53 / mitochondrial / L53mt / MRP-L53


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 Large ribosomal subunit protein mL54 / 39S ribosomal protein L54 / mitochondrial / L54mt / MRP-L54


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 Large ribosomal subunit protein mL55 / 39S ribosomal protein L55 / mitochondrial / L55mt / MRP-L55 / Mitochondrial large ribosomal subunit ...39S ribosomal protein L55 / mitochondrial / L55mt / MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m


Mass: 15160.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z7F7
#48: Protein Large ribosomal subunit protein mL63 / Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57 / Ribosomal protein 63 / ...Mitochondrial ribosomal protein 63 / Mitochondrial ribosomal protein L57 / Ribosomal protein 63 / mitochondrial / hMRP63


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 Large ribosomal subunit protein mL62 / 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 / Peptidyl-tRNA hydrolase ICT1


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 Large ribosomal subunit protein mL64 / 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 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 / Papillomavirus L2-interacting nuclear protein 1 / PLINP / 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
#51: Protein Large ribosomal subunit protein mL66 / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / 39S ribosomal protein S18a / MRP-S18-a / ...39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / 39S ribosomal protein S18a / MRP-S18-a / Mrps18a / S18mt-a / Large ribosomal subunit protein bS18a


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 Large ribosomal subunit protein mL65 / 39S ribosomal protein S30 / mitochondrial / MRP-S30 / S30mt / Large ribosomal subunit protein mS30 ...39S ribosomal protein S30 / mitochondrial / MRP-S30 / S30mt / 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

-
Mitochondrial ... , 3 types, 3 molecules LRuv

#14: 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
#53: Protein Mitochondrial assembly of ribosomal large subunit protein 1


Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3
#54: Protein Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Alternative MIEF1 protein / AltMIEF1 / MIEF1 microprotein / MIEF1-MP / alternative transcript ...Alternative MIEF1 protein / AltMIEF1 / MIEF1 microprotein / MIEF1-MP / alternative transcript upstream of MiD51 / AltMiD51


Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8

-
39S ribosomal protein ... , 2 types, 2 molecules LVLz

#18: 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
#44: Protein 39S ribosomal protein L52, mitochondrial


Mass: 13696.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8K7J6

-
Protein , 1 types, 1 molecules w

#55: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561

-
Non-polymers , 4 types, 100 molecules

#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 95 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-T1C / TIGECYCLINE


Mass: 587.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N5O8
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#59: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 55S mitoribosome with tigecycline / Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL
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

-
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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

CTF correctionDetails: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12156 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more