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- PDB-8pk0: human mitoribosomal large subunit assembly intermediate 1 with GT... -

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Basic information

Entry
Database: PDB / ID: 8pk0
Titlehuman mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7
Components
  • (39S ribosomal protein ...) x 45
  • (Mitochondrial ...) x 2
  • 16S rRNA + pre-H68-71 segment
  • 5-methylcytosine rRNA methyltransferase NSUN4
  • Acyl carrier protein, mitochondrial
  • CP tRNA-Val
  • GTP-binding protein 10
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • Large ribosomal subunit protein mL43
  • MIEF1 upstream open reading frame protein
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein 63, mitochondrial
  • Transcription termination factor 4, mitochondrial
KeywordsRIBOSOME / mitochondria / maturation / biogenesis / GTPBP7 / GTPBP10 / GTP Binding Protein 10 / OBGH2 / MTG1 / LSU
Function / homology
Function and homology information


regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation ...regulation of respiratory system process / rRNA modification in the mitochondrion / regulation of mitochondrial translation / negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / rRNA (cytosine-C5-)-methyltransferase activity / negative regulation of ribosome biogenesis / tRNA (cytidine-5-)-methyltransferase activity / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / rRNA methyltransferase activity / Respiratory electron transport / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / protein targeting to mitochondrion / Glyoxylate metabolism and glycine degradation / mitochondrial fission / camera-type eye development / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / rRNA methylation / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / Transferases; Transferring one-carbon groups; Methyltransferases / ribosomal large subunit biogenesis / methyltransferase activity / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / rRNA processing / double-stranded RNA binding / ribosome biogenesis / cell junction / chromosome / heart development / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / double-stranded DNA binding / endonuclease activity / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / synapse / calcium ion binding / regulation of DNA-templated transcription / nucleolus / GTP binding / magnesium ion binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / OBG-type GTPase / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / GTP1/OBG / Obg domain profile. / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic ...GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / OBG-type GTPase / GTP1/OBG domain / GTP-binding protein Obg/CgtA / GTP1/OBG domain superfamily / GTP1/OBG / Obg domain profile. / Mitochondrial termination factor repeats / Transcription termination factor, mitochondrial/chloroplastic / MTERF superfamily, mitochondrial/chloroplastic / mTERF / MIEF1-MP, LYR domain / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / : / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Ribosomal protein L37, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L55 / Mitochondrial ribosomal protein L46 NUDIX / 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 L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / 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 / Ribosomal protein L35, mitochondrial / MRPL44, double-stranded RNA binding domain / GTP-binding protein, orthogonal bundle domain superfamily / Tim44-like domain / Tim44-like domain / Tim44 / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / 50S ribosome-binding GTPase / GTP binding domain / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / : / Acyl carrier protein (ACP) / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 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 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Nucleotidyltransferase superfamily / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / Chem-PM8 / S-ADENOSYLMETHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / Chem-PM8 / S-ADENOSYLMETHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / GTP-binding protein 10 / 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 / Transcription termination factor 4, mitochondrial / Large ribosomal subunit protein mL55 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein mL52 / 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 / 5-methylcytosine rRNA methyltransferase NSUN4 / 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 / Mitochondrial ribosome-associated GTPase 1 / 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 uL18m / 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 uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein bL35m / Large ribosomal subunit protein uL15m / 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: 3.03 Å
AuthorsKummer, E. / Nguyen, T.G. / Ritter, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0067360 Denmark
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome.
Authors: Thu Giang Nguyen / Christina Ritter / Eva Kummer /
Abstract: Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ...Mitochondria contain their own genetic information and a dedicated translation system to express it. The mitochondrial ribosome is assembled from mitochondrial-encoded RNA and nuclear-encoded ribosomal proteins. Assembly is coordinated in the mitochondrial matrix by biogenesis factors that transiently associate with the maturing particle. Here, we present a structural snapshot of a large mitoribosomal subunit assembly intermediate containing 7 biogenesis factors including the GTPases GTPBP7 and GTPBP10. Our structure illustrates how GTPBP10 aids the folding of the ribosomal RNA during the biogenesis process, how this process is related to bacterial ribosome biogenesis, and why mitochondria require two biogenesis factors in contrast to only one in bacteria.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 2.0Jun 26, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / em_admin / em_entity_assembly / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _em_admin.last_update / _em_entity_assembly.entity_id_list / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_seq_align_beg_ins_code / _struct_ref_seq.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: 39S ribosomal protein L32, mitochondrial
T: 39S ribosomal protein L22, mitochondrial
u: Mitochondrial assembly of ribosomal large subunit protein 1
1: 39S ribosomal protein L33, mitochondrial
U: 39S ribosomal protein L23, mitochondrial
v: MIEF1 upstream open reading frame protein
2: 39S ribosomal protein L34, mitochondrial
V: 39S ribosomal protein L24, mitochondrial
w: Acyl carrier protein, mitochondrial
3: 39S ribosomal protein L35, mitochondrial
W: 39S ribosomal protein L27, mitochondrial
x: 5-methylcytosine rRNA methyltransferase NSUN4
5: 39S ribosomal protein L37, mitochondrial
X: 39S ribosomal protein L28, mitochondrial
y: Transcription termination factor 4, mitochondrial
6: 39S ribosomal protein L38, mitochondrial
Y: 39S ribosomal protein L47, mitochondrial
z: Mitochondrial ribosome-associated GTPase 1
7: 39S ribosomal protein L39, mitochondrial
Z: 39S ribosomal protein L30, mitochondrial
8: 39S ribosomal protein L40, mitochondrial
a: 39S ribosomal protein L42, mitochondrial
9: 39S ribosomal protein L41, mitochondrial
b: Large ribosomal subunit protein mL43
A: 16S rRNA + pre-H68-71 segment
c: 39S ribosomal protein L44, mitochondrial
B: CP tRNA-Val
d: 39S ribosomal protein L45, mitochondrial
D: 39S ribosomal protein L2, mitochondrial
e: 39S ribosomal protein L46, mitochondrial
E: 39S ribosomal protein L3, mitochondrial
f: 39S ribosomal protein L48, mitochondrial
F: 39S ribosomal protein L4, mitochondrial
g: 39S ribosomal protein L49, mitochondrial
H: 39S ribosomal protein L9, mitochondrial
h: 39S ribosomal protein L50, mitochondrial
I: 39S ribosomal protein L10, mitochondrial
i: 39S ribosomal protein L51, mitochondrial
J: 39S ribosomal protein L11, mitochondrial
j: 39S ribosomal protein L52, mitochondrial
K: 39S ribosomal protein L13, mitochondrial
k: 39S ribosomal protein L53, mitochondrial
L: 39S ribosomal protein L14, mitochondrial
l: 39S ribosomal protein L54, mitochondrial
M: 39S ribosomal protein L15, mitochondrial
m: 39S ribosomal protein L55, mitochondrial
N: 39S ribosomal protein L16, mitochondrial
o: Ribosomal protein 63, mitochondrial
O: 39S ribosomal protein L17, mitochondrial
p: Peptidyl-tRNA hydrolase ICT1, mitochondrial
P: 39S ribosomal protein L18, mitochondrial
q: Growth arrest and DNA damage-inducible proteins-interacting protein 1
Q: 39S ribosomal protein L19, mitochondrial
r: 39S ribosomal protein S18a, mitochondrial
R: 39S ribosomal protein L20, mitochondrial
s: 39S ribosomal protein S30, mitochondrial
S: 39S ribosomal protein L21, mitochondrial
t: GTP-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,963,043169
Polymers1,958,31458
Non-polymers4,729111
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area367540 Å2
ΔGint-3103 kcal/mol
Surface area585250 Å2

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Components

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39S ribosomal protein ... , 45 types, 45 molecules 0T1U2V3W5X6Y7Z8a9cdDeEfFgHhIiJ...

#1: Protein 39S ribosomal protein L32, mitochondrial / L32mt / 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 L22, mitochondrial / L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ...L22mt / MRP-L22 / 39S ribosomal protein L25 / mitochondrial / L25mt / MRP-L25 / Mitochondrial large ribosomal subunit protein uL22m


Mass: 23683.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWU5
#4: Protein 39S ribosomal protein L33, mitochondrial / L33mt / 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
#5: Protein 39S ribosomal protein L23, mitochondrial / L23mt / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein ...L23mt / MRP-L23 / L23 mitochondrial-related protein / Mitochondrial large ribosomal subunit protein uL23m / Ribosomal protein L23-like


Mass: 17849.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16540
#7: Protein 39S ribosomal protein L34, mitochondrial / L34mt / 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
#8: Protein 39S ribosomal protein L24, mitochondrial / L24mt / 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
#10: Protein 39S ribosomal protein L35, mitochondrial / L35mt / 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
#11: Protein 39S ribosomal protein L27, mitochondrial / L27mt / 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
#13: Protein 39S ribosomal protein L37, mitochondrial / L37mt / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / L2mt / MRP-L2 / Mitochondrial large ...L37mt / MRP-L37 / 39S ribosomal protein L2 / mitochondrial / L2mt / 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
#14: Protein 39S ribosomal protein L28, mitochondrial / L28mt / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / ...L28mt / 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
#16: Protein 39S ribosomal protein L38, mitochondrial / L38mt / 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
#17: Protein 39S ribosomal protein L47, mitochondrial / L47mt / MRP-L47 / Mitochondrial large ribosomal subunit protein uL29m / Nasopharyngeal carcinoma ...L47mt / 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
#19: Protein 39S ribosomal protein L39, mitochondrial / L39mt / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / L5mt / MRP-L5 / Mitochondrial large ...L39mt / MRP-L39 / 39S ribosomal protein L5 / mitochondrial / L5mt / 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
#20: Protein 39S ribosomal protein L30, mitochondrial / L30mt / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / L28mt / MRP-L28 / Mitochondrial large ...L30mt / MRP-L30 / 39S ribosomal protein L28 / mitochondrial / L28mt / 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
#21: Protein 39S ribosomal protein L40, mitochondrial / L40mt / MRP-L40 / Mitochondrial large ribosomal subunit protein mL40 / Nuclear localization signal- ...L40mt / 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
#22: Protein 39S ribosomal protein L42, mitochondrial / L42mt / MRP-L42 / 39S ribosomal protein L31 / mitochondrial / L31mt / MRP-L31 / Mitochondrial large ...L42mt / MRP-L42 / 39S ribosomal protein L31 / mitochondrial / L31mt / 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
#23: Protein 39S ribosomal protein L41, mitochondrial / L41mt / MRP-L41 / 39S ribosomal protein L27 homolog / Bcl-2-interacting mitochondrial ribosomal ...L41mt / 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
#26: Protein 39S ribosomal protein L44, mitochondrial / L44mt / 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
#28: Protein 39S ribosomal protein L45, mitochondrial / L45mt / 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
#29: Protein 39S ribosomal protein L2, mitochondrial / L2mt / 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
#30: Protein 39S ribosomal protein L46, mitochondrial / L46mt / 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
#31: Protein 39S ribosomal protein L3, mitochondrial / L3mt / 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
#32: Protein 39S ribosomal protein L48, mitochondrial / L48mt / MRP-L48 / Mitochondrial large ribosomal subunit protein mL48


Mass: 23970.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96GC5
#33: Protein 39S ribosomal protein L4, mitochondrial / L4mt / 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
#34: Protein 39S ribosomal protein L49, mitochondrial / L49mt / 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
#35: Protein 39S ribosomal protein L9, mitochondrial / L9mt / 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
#36: Protein 39S ribosomal protein L50, mitochondrial / L50mt / 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
#37: Protein 39S ribosomal protein L10, mitochondrial / L10mt / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / L8mt / MRP-L8 / Mitochondrial large ...L10mt / MRP-L10 / 39S ribosomal protein L8 / mitochondrial / L8mt / 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
#38: Protein 39S ribosomal protein L51, mitochondrial / L51mt / 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
#39: Protein 39S ribosomal protein L11, mitochondrial / L11mt / 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
#40: Protein 39S ribosomal protein L52, mitochondrial / L52mt / MRP-L52 / Mitochondrial large ribosomal subunit protein mL52


Mass: 13682.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86TS9
#41: Protein 39S ribosomal protein L13, mitochondrial / L13mt / MRP-L13 / Mitochondrial large ribosomal subunit protein uL13m


Mass: 20765.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD1
#42: Protein 39S ribosomal protein L53, mitochondrial / L53mt / MRP-L53 / Mitochondrial large ribosomal subunit protein mL53


Mass: 12167.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EL3
#43: Protein 39S ribosomal protein L14, mitochondrial / L14mt / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / L32mt / MRP-L32 / Mitochondrial large ...L14mt / MRP-L14 / 39S ribosomal protein L32 / mitochondrial / L32mt / 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
#44: Protein 39S ribosomal protein L54, mitochondrial / L54mt / 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
#45: Protein 39S ribosomal protein L15, mitochondrial / L15mt / 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
#46: Protein 39S ribosomal protein L55, mitochondrial / L55mt / MRP-L55 / Mitochondrial large ribosomal subunit protein bL31m / Mitochondrial large ...L55mt / 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
#47: Protein 39S ribosomal protein L16, mitochondrial / L16mt / 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
#49: Protein 39S ribosomal protein L17, mitochondrial / L17mt / 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
#51: Protein 39S ribosomal protein L18, mitochondrial / L18mt / MRP-L18 / Mitochondrial large ribosomal subunit protein uL18m


Mass: 20607.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H0U6
#53: Protein 39S ribosomal protein L19, mitochondrial / L19mt / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / L15mt / MRP-L15 / Mitochondrial large ...L19mt / MRP-L19 / 39S ribosomal protein L15 / mitochondrial / L15mt / 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 S18a, mitochondrial / MRP-S18-a / Mrps18a / S18mt-a / 39S ribosomal protein S18-3 / mitochondrial / MRP-S18-3 / ...MRP-S18-a / Mrps18a / 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
#55: Protein 39S ribosomal protein L20, mitochondrial / L20mt / 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
#56: Protein 39S ribosomal protein S30, mitochondrial / MRP-S30 / S30mt / Mitochondrial large ribosomal subunit protein mL65 / Mitochondrial large ...MRP-S30 / 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
#57: Protein 39S ribosomal protein L21, mitochondrial / L21mt / 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

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Mitochondrial ... , 2 types, 2 molecules uz

#3: 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
#18: Protein Mitochondrial ribosome-associated GTPase 1 / GTP-binding protein 7 / Mitochondrial GTPase 1


Mass: 37292.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BT17

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Protein , 9 types, 9 molecules vwxybopqt

#6: Protein MIEF1 upstream open reading frame protein


Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8
#9: 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
#12: Protein 5-methylcytosine rRNA methyltransferase NSUN4 / NOL1/NOP2/Sun domain family member 4


Mass: 43140.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q96CB9, Transferases; Transferring one-carbon groups; Methyltransferases
#15: Protein Transcription termination factor 4, mitochondrial / Mitochondrial transcription termination factor 4 / mTERF domain-containing protein 2


Mass: 44012.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z6M4
#24: Protein Large ribosomal subunit protein mL43 / 39S ribosomal protein L43 / mitochondrial / L43mt / MRP-L43 / Mitochondrial ribosomal protein bMRP36a


Mass: 23352.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983
#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
#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
#52: 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 / 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
#58: Protein GTP-binding protein 10 / Protein obg homolog 2 / ObgH2


Mass: 42996.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A4D1E9

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RNA chain , 2 types, 2 molecules AB

#25: RNA chain 16S rRNA + pre-H68-71 segment


Mass: 509550.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1858624182
#27: RNA chain CP tRNA-Val


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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Non-polymers , 6 types, 111 molecules

#59: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-PM8 / S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE


Mass: 496.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H41N2O7PS
#61: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#62: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#63: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: Mg
#64: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K

-
Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: large mitoribosomal subunit biogenesis intermediate with GTPBP10, GTPBP7, NSUN4-MTERF4, ACP-module
Type: RIBOSOME
Entity ID: #1, #4, #7, #10, #13, #16, #19, #21, #23, #27, #29, #31, #33, #35, #37, #39, #41, #43, #45, #47, #49, #51, #53, #55, #57, #2, #5, #8, #11, #14, #17, #20, #22, #26, #28, #30, #32, #34, #36, ...Entity ID: #1, #4, #7, #10, #13, #16, #19, #21, #23, #27, #29, #31, #33, #35, #37, #39, #41, #43, #45, #47, #49, #51, #53, #55, #57, #2, #5, #8, #11, #14, #17, #20, #22, #26, #28, #30, #32, #34, #36, #38, #40, #42, #44, #46, #48, #50, #52, #54, #56, #58, #3, #6, #9, #12, #15, #18
Source: NATURAL
Molecular weightValue: 1.9 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31656 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002117075
ELECTRON MICROSCOPYf_angle_d0.476165518
ELECTRON MICROSCOPYf_dihedral_angle_d13.21649491
ELECTRON MICROSCOPYf_chiral_restr0.03519334
ELECTRON MICROSCOPYf_plane_restr0.00415718

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