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- PDB-7l20: Cryo-EM structure of the human 39S mitoribosomal subunit in compl... -

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Basic information

Entry
Database: PDB / ID: 7l20
TitleCryo-EM structure of the human 39S mitoribosomal subunit in complex with RRFmt and EF-G2mt.
Components
  • (39S ribosomal protein ...) x 46
  • 16S rRNA mitochondrial
  • 39 S P-site finger
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • Mitochondrial ribosomal protein L18, isoform CRA_b
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein 63, mitochondrial
  • Ribosome-recycling factor, mitochondrial
  • Ribosome-releasing factor 2, mitochondrial
  • cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA
  • tRNAval
KeywordsRIBOSOME / Cryo-EM / Mammalian / mito-ribosome / mtEFg2 / mtRRF
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 / ribosome disassembly / peptidyl-tRNA hydrolase activity / mitochondrial translation / ribosomal large subunit binding / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / GTPase activity / mRNA binding / apoptotic process / positive regulation of DNA-templated transcription / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Ribosome-releasing factor 2, mitochondrial / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / : / Elongation factor G domain 2 / : / : / Ribosomal protein L55, mitochondrial ...Ribosome-releasing factor 2, mitochondrial / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / : / Elongation factor G domain 2 / : / : / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / : / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Elongation factor G, domain III / EFG, domain V / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature.
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / 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 ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / 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 / Ribosome-releasing factor 2, mitochondrial / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein mL38 / Ribosome-recycling factor, mitochondrial / 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: 3.15 Å
AuthorsAgrawal, E. / Koripella, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 GM61576 United States
CitationJournal: Nat Commun / Year: 2021
Title: Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance.
Authors: Ravi Kiran Koripella / Ayush Deep / Ekansh K Agrawal / Pooja Keshavan / Nilesh K Banavali / Rajendra K Agrawal /
Abstract: Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we ...Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRF) and a recycling-specific homolog of elongation factor G (EF-G2). These structures clarify an unusual role of a mitochondria-specific segment of RRF, identify the structural distinctions that confer functional specificity to EF-G2, and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2 is markedly different from that of mitochondrial elongation factor EF-G1, suggesting that the two human EF-Gs have evolved diversely to negate the effect of a bacterial antibiotic.
History
DepositionDec 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,906,439164
Polymers1,903,24358
Non-polymers3,197106
Water00
1
A: 16S rRNA mitochondrial
B: tRNAval
D: 39S ribosomal protein L2, mitochondrial
F: 39S ribosomal protein L4, mitochondrial
H: 39S ribosomal protein L9, mitochondrial
K: 39S ribosomal protein L13, mitochondrial
L: 39S ribosomal protein L14, mitochondrial
M: 39S ribosomal protein L15, mitochondrial
O: 39S ribosomal protein L17, mitochondrial
R: 39S ribosomal protein L20, mitochondrial
S: 39S ribosomal protein L21, mitochondrial
T: 39S ribosomal protein L22, 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
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
8: 39S ribosomal protein L40, mitochondrial
b: 39S ribosomal protein L43, mitochondrial
e: 39S ribosomal protein L46, mitochondrial
g: 39S ribosomal protein L49, mitochondrial
i: 39S ribosomal protein L51, mitochondrial
j: cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA
m: 39S ribosomal protein L55, mitochondrial
o: Ribosomal protein 63, mitochondrial
q: Growth arrest and DNA damage-inducible proteins-interacting protein 1
r: 39S ribosomal protein S18a, mitochondrial
J: 39S ribosomal protein L11, mitochondrial
I: 39S ribosomal protein L10, mitochondrial
N: 39S ribosomal protein L16, mitochondrial
P: Mitochondrial ribosomal protein L18, isoform CRA_b
U: 39S ribosomal protein L23, mitochondrial
V: 39S ribosomal protein L24, mitochondrial
E: 39S ribosomal protein L3, mitochondrial
5: 39S ribosomal protein L37, mitochondrial
6: 39S ribosomal protein L38, mitochondrial
7: 39S ribosomal protein L39, mitochondrial
9: 39S ribosomal protein L41, mitochondrial
a: 39S ribosomal protein L42, mitochondrial
c: 39S ribosomal protein L44, mitochondrial
d: 39S ribosomal protein L45, mitochondrial
f: 39S ribosomal protein L48, mitochondrial
h: 39S ribosomal protein L50, mitochondrial
k: 39S ribosomal protein L53, mitochondrial
l: 39S ribosomal protein L54, mitochondrial
p: Peptidyl-tRNA hydrolase ICT1, mitochondrial
s: 39S ribosomal protein S30, mitochondrial
Q: 39S ribosomal protein L19, mitochondrial
u: 39 S P-site finger
TA: 39S ribosomal protein L12, mitochondrial
TB: 39S ribosomal protein L12, mitochondrial
z: Ribosome-recycling factor, mitochondrial
w: Ribosome-releasing factor 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,885,061163
Polymers1,881,86457
Non-polymers3,197106
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area366400 Å2
ΔGint-3241 kcal/mol
Surface area580540 Å2

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 16S rRNA mitochondrial


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


Mass: 23266.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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39S ribosomal protein ... , 46 types, 48 molecules DFHKLMORSTWXYZ012348begimrJINU...

#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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: 30090.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#28: 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
#31: 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
#32: 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
#33: 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
#34: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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
#49: 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
#51: 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
#52: 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
#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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Protein , 8 types, 8 molecules joqPpuzw

#27: 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
#29: 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
#30: 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
#35: 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
#50: 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
#53: Protein 39 S P-site finger


Mass: 5549.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#55: Protein Ribosome-recycling factor, mitochondrial / RRF / Ribosome-releasing factor / mitochondrial


Mass: 22590.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96E11
#56: Protein Ribosome-releasing factor 2, mitochondrial / RRF2mt / Elongation factor G 2 / mitochondrial / EF-G2mt / mEF-G 2 / Elongation factor G2 / hEFG2


Mass: 77306.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969S9

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Non-polymers , 3 types, 106 molecules

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


Mass: 24.305 Da / Num. of mol.: 102 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#59: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN
Has protein modificationY

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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: Cryo-EM structure of Mammalian Mitochondrial ribosome complex with mtEFG-2 and mtRRF
Type: RIBOSOME
Details: Cryo-EM structure of Mammalian Mitochondrial ribosome complex with mtEFG-2 and mtRRF-Class-3
Entity ID: #1-#56 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
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: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER
Image recordingElectron dose: 71 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132008 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

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