[English] 日本語
Yorodumi
- PDB-7a5j: Structure of the split human mitoribosomal large subunit with P-a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a5j
TitleStructure of the split human mitoribosomal large subunit with P-and E-site mt-tRNAs
Components
  • (39S ribosomal protein ...) x 45
  • (Mitochondrial ...) x 2
  • (Unknown protein/protein ...) x 3
  • 16S rRNA
  • 50S ribosomal protein L1
  • Acyl carrier protein, mitochondrial
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • MIEF1 upstream open reading frame protein
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Ribosomal protein 63, mitochondrial
  • cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA
  • mt-tRNA
  • mt-tRNAVal
  • nascent chain
KeywordsRIBOSOME / mitochondrial ribosome / ribosome stalling / cryo-EM
Function / homology
Function and homology information


negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / negative regulation of ribosome biogenesis / protein lipoylation / 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 / negative regulation of ribosome biogenesis / protein lipoylation / 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 / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit / mitochondrial fission / peptidyl-tRNA hydrolase / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / 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 / ribosomal large subunit binding / acyl carrier activity / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / anatomical structure morphogenesis / RNA processing / rescue of stalled cytosolic ribosome / Mitochondrial protein degradation / aerobic respiration / fatty acid binding / cellular response to leukemia inhibitory factor / ribosomal large subunit biogenesis / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / cell junction / regulation of translation / large ribosomal subunit / double-stranded RNA binding / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / tRNA binding / negative regulation of translation / mitochondrial inner membrane / 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 / 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 / Mitochondrial ribosomal protein L37 / 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 L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / 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 / : / Ribosomal protein L1, bacterial-type / 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 / Beta-grasp domain superfamily / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NTF2-like domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Acyl carrier protein (ACP) / Ribosomal protein L1, 3-layer alpha/beta-sandwich / NUDIX hydrolase-like domain superfamily / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P
Similarity search - Domain/homology
: / : / 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 ...: / : / 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 uL1 / 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)
Thermus thermophilus HB27 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDesai, N. / Yang, H. / Chandrasekaran, V. / Kazi, R. / Minczuk, M. / Ramakrishnan, V.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
Louis-Jeantet Foundation United Kingdom
CitationJournal: Science / Year: 2020
Title: Elongational stalling activates mitoribosome-associated quality control.
Authors: Nirupa Desai / Hanting Yang / Viswanathan Chandrasekaran / Razina Kazi / Michal Minczuk / V Ramakrishnan /
Abstract: The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a ...The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase.
History
DepositionAug 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / em_entity_assembly / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_asym / struct_conf / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_entity_assembly.entity_id_list / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_nat.common_name / _entity_src_nat.pdbx_organism_scientific / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11645
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: 39S ribosomal protein L2, mitochondrial
E: 39S ribosomal protein L3, mitochondrial
F: 39S ribosomal protein L4, mitochondrial
H: 39S ribosomal protein L9, mitochondrial
I: 39S ribosomal protein L10, mitochondrial
J: 39S ribosomal protein L11, mitochondrial
K: 39S ribosomal protein L13, mitochondrial
L: 39S ribosomal protein L14, mitochondrial
M: 39S ribosomal protein L15, mitochondrial
N: 39S ribosomal protein L16, mitochondrial
O: 39S ribosomal protein L17, mitochondrial
P: Mitochondrial ribosomal protein L18, isoform CRA_b
Q: 39S ribosomal protein L19, mitochondrial
R: 39S ribosomal protein L20, mitochondrial
S: 39S ribosomal protein L21, mitochondrial
T: 39S ribosomal protein L22, mitochondrial
U: 39S ribosomal protein L23, mitochondrial
V: 39S ribosomal protein L24, mitochondrial
W: 39S ribosomal protein L27, mitochondrial
X: 39S ribosomal protein L28, mitochondrial
Y: 39S ribosomal protein L47, mitochondrial
Z: 39S ribosomal protein L30, mitochondrial
0: 39S ribosomal protein L32, mitochondrial
1: 39S ribosomal protein L33, mitochondrial
2: 39S ribosomal protein L34, mitochondrial
3: 39S ribosomal protein L35, mitochondrial
4: 39S ribosomal protein L36, mitochondrial
5: 39S ribosomal protein L37, mitochondrial
6: 39S ribosomal protein L38, mitochondrial
7: 39S ribosomal protein L39, mitochondrial
8: 39S ribosomal protein L40, mitochondrial
9: 39S ribosomal protein L41, mitochondrial
a: 39S ribosomal protein L42, mitochondrial
b: 39S ribosomal protein L43, mitochondrial
c: 39S ribosomal protein L44, mitochondrial
d: 39S ribosomal protein L45, mitochondrial
e: 39S ribosomal protein L46, mitochondrial
f: 39S ribosomal protein L48, mitochondrial
g: 39S ribosomal protein L49, mitochondrial
h: 39S ribosomal protein L50, mitochondrial
i: 39S ribosomal protein L51, mitochondrial
j: cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNA
k: 39S ribosomal protein L53, mitochondrial
l: 39S ribosomal protein L54, mitochondrial
m: 39S ribosomal protein L55, mitochondrial
o: Ribosomal protein 63, mitochondrial
p: Peptidyl-tRNA hydrolase ICT1, mitochondrial
q: Growth arrest and DNA damage-inducible proteins-interacting protein 1
r: 39S ribosomal protein S18a, mitochondrial
s: 39S ribosomal protein S30, mitochondrial
t: Unknown protein/protein extension
u: Mitochondrial assembly of ribosomal large subunit protein 1
v: MIEF1 upstream open reading frame protein
w: Acyl carrier protein, mitochondrial
n: 50S ribosomal protein L1
A: 16S rRNA
B: mt-tRNAVal
Y2: nascent chain
C: 39S ribosomal protein L9, mitochondrial
G: mt-tRNA
y: Unknown protein/protein extension
z: unknown protein/protein extension
x: mt-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,898,323164
Polymers1,895,72763
Non-polymers2,595101
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
39S ribosomal protein ... , 45 types, 46 molecules DEFHCIJKLMNOQRSTUVWXYZ01234567...

#1: 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
#2: 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
#3: 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
#4: Protein 39S ribosomal protein L9, mitochondrial / MRP-L9 / Mitochondrial large ribosomal subunit protein bL9m


Mass: 30296.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BYD2
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: Protein 39S ribosomal protein L28, mitochondrial / MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / ...MRP-L28 / Melanoma antigen p15 / Melanoma-associated antigen recognized by T-lymphocytes / Mitochondrial large ribosomal subunit protein bL28m


Mass: 30202.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13084
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#43: 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
#44: 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
#45: 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
#49: 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
#50: 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

-
Mitochondrial ... , 2 types, 2 molecules Pu

#12: 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
#52: 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

-
Protein , 7 types, 7 molecules jopqvwn

#42: 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
#46: 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
#47: 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
#48: Protein Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6- ...39S ribosomal protein L59 / mitochondrial / MRP-L59 / CKII beta-associating protein / CR6-interacting factor 1 / CRIF1 / Mitochondrial large ribosomal subunit protein mL64 / Papillomavirus L2-interacting nuclear protein 1 / PLINP-1 / p53-responsive gene 6 protein


Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8
#53: Protein 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
#54: Protein Acyl carrier protein, mitochondrial / ACP / CI-SDAP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit


Mass: 17774.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14561
#55: Protein 50S ribosomal protein L1


Mass: 24867.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72GV9

-
Unknown protein/protein ... , 3 types, 3 molecules tyz

#51: Protein/peptide Unknown protein/protein extension


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#60: Protein/peptide Unknown protein/protein extension


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#61: Protein/peptide unknown protein/protein extension


Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
RNA chain , 3 types, 4 molecules ABGx

#56: RNA chain 16S rRNA


Mass: 500019.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1025814679
#57: RNA chain mt-tRNAVal


Mass: 22022.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 1485738021
#59: RNA chain mt-tRNA


Mass: 23378.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Protein/peptide , 1 types, 1 molecules Y2

#58: Protein/peptide nascent chain


Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Non-polymers , 4 types, 101 molecules

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


Mass: 24.305 Da / Num. of mol.: 92 / Source method: obtained synthetically / Formula: Mg
#63: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#64: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#65: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human mitoribosomeRIBOSOME#1-#53, #55-#610MULTIPLE SOURCES
2ribosomeRIBOSOME#1-#53, #56-#611NATURAL
350S ribosomal protein L1RIBOSOME#551NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)262724
Buffer solutionpH: 7.4
SpecimenConc.: 0.4 mg/ml / Embedding 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
Image recordingElectron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54398 / 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