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- PDB-6swa: Mus musculus brain neocortex ribosome 60S bound to Ebp1 -

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Basic information

Entry
Database: PDB / ID: 6swa
TitleMus musculus brain neocortex ribosome 60S bound to Ebp1
Components
  • (60S ribosomal protein ...) x 38
  • (Ribosomal protein ...) x 4
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Proliferation-associated protein 2G4
KeywordsRIBOSOME / 60S / EBP1 / neurodevelopment / neocortex / 80S / peptide tunnel exit
Function / homology
Function and homology information


5.8S rRNA binding / Protein hydroxylation / negative regulation of protein neddylation / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / selenocysteine insertion sequence binding / L13a-mediated translational silencing of Ceruloplasmin expression ...5.8S rRNA binding / Protein hydroxylation / negative regulation of protein neddylation / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / selenocysteine insertion sequence binding / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / translation at postsynapse / A band / aminoacyl-tRNA synthetase multienzyme complex / embryonic brain development / translation at presynapse / response to aldosterone / exit from mitosis / optic nerve development / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / peroxisome proliferator activated receptor binding / cellular response to actinomycin D / axial mesoderm development / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / protein-DNA complex disassembly / 90S preribosome assembly / alpha-beta T cell differentiation / GAIT complex / TORC2 complex binding / G1 to G0 transition / middle ear morphogenesis / growth factor binding / cell-substrate adhesion / homeostatic process / macrophage chemotaxis / lung morphogenesis / positive regulation of natural killer cell proliferation / cellular response to dexamethasone stimulus / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / ribonucleoprotein complex binding / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of G1/S transition of mitotic cell cycle / protein targeting / protein-RNA complex assembly / maturation of LSU-rRNA / translation regulator activity / Neutrophil degranulation / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cytosolic ribosome / liver regeneration / cellular response to interleukin-4 / ossification / cellular response to amino acid starvation / regulation of signal transduction by p53 class mediator / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / innate immune response in mucosa / skeletal system development / mRNA 3'-UTR binding / positive regulation of cell differentiation / sensory perception of sound / bone development / cellular response to type II interferon / mRNA 5'-UTR binding / multicellular organism growth / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / rRNA processing / transcription corepressor activity / regulation of translation / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / large ribosomal subunit / antibacterial humoral response / presynapse / retina development in camera-type eye / cell body / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / response to lipopolysaccharide / killing of cells of another organism / cytosolic large ribosomal subunit / nucleic acid binding / defense response to Gram-negative bacterium / cytoplasmic translation / tRNA binding / cell population proliferation / negative regulation of translation / postsynaptic density / postsynapse / rRNA binding / protein stabilization
Similarity search - Function
PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e ...PA2G4 family / : / Peptidase M24A, methionine aminopeptidase, subfamily 2, binding site / Methionine aminopeptidase subfamily 2 signature. / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L28e / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / : / Ribosomal protein L10e signature. / Ribosomal protein L6e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / : / Ribosomal L40e family / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / Ribosomal Protein L6, KOW domain / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L7A/L8 / : / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein L6e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L6E / : / Ribosomal protein L30/YlxQ / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L18e
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein eL36 / Proliferation-associated protein 2G4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL39 / 60S ribosomal protein L27 / Ubiquitin-ribosomal protein eL40 fusion protein / Ribosomal protein L36A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL38
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKraushar, M.L. / Sprink, T.
Funding support Germany, 4items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)190-2016 Germany
Alexander von Humboldt Foundation Germany
European Union (EU)iNEXT (PID: 2227) Germany
European Union (EU)Instruct-ERIC Pilot R&D Project (APPID: 232) Germany
CitationJournal: Mol Cell / Year: 2021
Title: Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.
Authors: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / ...Authors: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / Theres Schaub / Agnieszka Münster-Wandowski / Jörg Bürger / Ekaterina Borisova / Hiroshi Yamamoto / Mladen-Roko Rasin / Uwe Ohler / Dieter Beule / Thorsten Mielke / Victor Tarabykin / Markus Landthaler / Günter Kramer / Imre Vida / Matthias Selbach / Christian M T Spahn /
Abstract: Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during ...Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / cell / citation / citation_author / em_entity_assembly / em_entity_assembly_naturalsource / em_software / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_audit_support / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct / struct_conf / struct_conn / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _cell.Z_PDB / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_entity_assembly.name / _em_entity_assembly_naturalsource.id / _em_entity_assembly_naturalsource.strain / _em_software.category / _em_software.fitting_id / _em_software.imaging_id / _em_software.name / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.common_name / _entity_src_nat.pdbx_end_seq_num / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly_prop.value / _struct.title / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.text / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: 60S ribosomal protein L8
B: 60S ribosomal protein L3
C: 60S ribosomal protein L4
D: 60S ribosomal protein L5
E: 60S ribosomal protein L6
F: 60S ribosomal protein L7
G: 60S ribosomal protein L7a
H: 60S ribosomal protein L9
I: 60S ribosomal protein L10
J: 60S ribosomal protein L11
K: 60S ribosomal protein L13
L: 60S ribosomal protein L14
M: 60S ribosomal protein L15
N: 60S ribosomal protein L13a
O: 60S ribosomal protein L17
P: 60S ribosomal protein L18
Q: 60S ribosomal protein L18a
R: 60S ribosomal protein L21
S: 60S ribosomal protein L22
T: 60S ribosomal protein L23
U: 60S ribosomal protein L24
V: 60S ribosomal protein L23a
W: Ribosomal protein L26
X: 60S ribosomal protein L27
Y: 60S ribosomal protein L27a
Z: 60S ribosomal protein L29
a: 60S ribosomal protein L30
b: 60S ribosomal protein L31
c: 60S ribosomal protein L32
d: 60S ribosomal protein L35a
e: 60S ribosomal protein L34
f: 60S ribosomal protein L35
g: 60S ribosomal protein L36
h: 60S ribosomal protein L37
i: 60S ribosomal protein L38
j: Ribosomal protein L39
k: 60S ribosomal protein L40
l: 60S ribosomal protein L41
m: Ribosomal protein L36A
n: Ribosomal protein L37a
o: 60S ribosomal protein L19
p: 60S ribosomal protein L28
q: 28S ribosomal RNA
r: 5.8S ribosomal RNA
s: 5S ribosomal RNA
t: Proliferation-associated protein 2G4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,043,922296
Polymers2,037,72246
Non-polymers6,200250
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area408260 Å2
ΔGint-5138 kcal/mol
Surface area711820 Å2
MethodPISA

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Components

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60S ribosomal protein ... , 38 types, 38 molecules ABCDEFGHIJKLMNOPQRSTUVXYZabcde...

#1: Protein 60S ribosomal protein L8


Mass: 27456.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62918
#2: Protein 60S ribosomal protein L3 / J1 protein


Mass: 45223.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P27659
#3: Protein 60S ribosomal protein L4


Mass: 41321.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D8E6
#4: Protein 60S ribosomal protein L5


Mass: 34129.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47962
#5: Protein 60S ribosomal protein L6 / TAX-responsive enhancer element-binding protein 107 / TAXREB107


Mass: 22359.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47911
#6: Protein 60S ribosomal protein L7


Mass: 27674.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14148
#7: Protein 60S ribosomal protein L7a / Surfeit locus protein 3


Mass: 26705.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P12970
#8: Protein 60S ribosomal protein L9


Mass: 21788.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51410
#9: Protein 60S ribosomal protein L10 / Protein QM homolog / Ribosomal protein L10


Mass: 24381.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV3
#10: Protein 60S ribosomal protein L11


Mass: 19270.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CXW4
#11: Protein 60S ribosomal protein L13 / A52


Mass: 23617.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47963
#12: Protein 60S ribosomal protein L14


Mass: 16301.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CR57
#13: Protein 60S ribosomal protein L15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CZM2
#14: Protein 60S ribosomal protein L13a / Transplantation antigen P198 / Tum-P198 antigen


Mass: 22748.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19253
#15: Protein 60S ribosomal protein L17


Mass: 17758.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CPR4
#16: Protein 60S ribosomal protein L18


Mass: 21411.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35980
#17: Protein 60S ribosomal protein L18a


Mass: 20631.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62717
#18: Protein 60S ribosomal protein L21


Mass: 18274.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O09167
#19: Protein 60S ribosomal protein L22 / Heparin-binding protein HBp15


Mass: 11738.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P67984
#20: Protein 60S ribosomal protein L23


Mass: 13828.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62830
#21: Protein 60S ribosomal protein L24


Mass: 7381.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BP67
#22: Protein 60S ribosomal protein L23a


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62751
#24: Protein 60S ribosomal protein L27


Mass: 15647.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5BLJ9
#25: Protein 60S ribosomal protein L27a / L29


Mass: 16517.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P14115
#26: Protein 60S ribosomal protein L29


Mass: 7964.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47915
#27: Protein 60S ribosomal protein L30


Mass: 10811.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62889
#28: Protein 60S ribosomal protein L31


Mass: 12506.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62900
#29: Protein 60S ribosomal protein L32


Mass: 15179.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62911
#30: Protein 60S ribosomal protein L35a


Mass: 12449.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: O55142
#31: Protein 60S ribosomal protein L34


Mass: 12993.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1R9
#32: Protein 60S ribosomal protein L35


Mass: 14464.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6ZWV7
#33: Protein 60S ribosomal protein L36


Mass: 11489.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P47964
#34: Protein 60S ribosomal protein L37


Mass: 9864.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D823
#35: Protein 60S ribosomal protein L38


Mass: 8093.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JJI8
#37: Protein/peptide 60S ribosomal protein L40 / CEP52 / Ubiquitin / Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin-60S ...CEP52 / Ubiquitin / Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin-60S ribosomal protein L40


Mass: 5957.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5M9K3
#38: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62947
#41: Protein 60S ribosomal protein L19


Mass: 22097.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P84099
#42: Protein 60S ribosomal protein L28


Mass: 14009.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P41105

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Ribosomal protein ... , 4 types, 4 molecules Wjmn

#23: Protein Ribosomal protein L26


Mass: 15161.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q4FZH2
#36: Protein/peptide Ribosomal protein L39


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q505A8
#39: Protein Ribosomal protein L36A


Mass: 12345.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5M9P1
#40: Protein Ribosomal protein L37a


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q4VAF2

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RNA chain , 3 types, 3 molecules qrs

#43: RNA chain 28S ribosomal RNA


Mass: 1170200.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We used the Oryctolagus cuniculus sequence to model the Mus musculus 28S ribosomal RNA
Source: (natural) Mus musculus (house mouse)
#44: RNA chain 5.8S ribosomal RNA


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We used the Oryctolagus cuniculus sequence to model the Mus musculus 5.8S ribosomal RNA
Source: (natural) Mus musculus (house mouse) / References: GenBank: 34447123
#45: RNA chain 5S ribosomal RNA


Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We used the Oryctolagus cuniculus sequence to model the Mus musculus 5S ribosomal RNA
Source: (natural) Mus musculus (house mouse) / References: GenBank: 1720429767

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Protein , 1 types, 1 molecules t

#46: Protein Proliferation-associated protein 2G4 / IRES-specific cellular trans-acting factor 45 kDa / ITAF45 / Mpp1 / Proliferation-associated ...IRES-specific cellular trans-acting factor 45 kDa / ITAF45 / Mpp1 / Proliferation-associated protein 1 / Protein p38-2G4


Mass: 39388.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P50580

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Non-polymers , 2 types, 250 molecules

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


Mass: 24.305 Da / Num. of mol.: 247 / Source method: obtained synthetically / Formula: Mg
#48: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: Mus musculus postnatal day 0 brain neocortex 80S ribosome bound to Ebp1
Type: RIBOSOME / Entity ID: #1-#46 / Source: NATURAL
Molecular weightValue: 3.2 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD1 / Cellular location: cytoplasm / Organ: brain / Tissue: neocortex
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2100 mMpotassium chlorideKCl1
310 mMmagnesium chlorideMgCl21
420 mMDithiothreitol1
50.04 mMSpermine1
60.5 mMSpermidine1
70.1 mg/mlcycloheximide1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 100 divisions/in. / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 31000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 20 sec. / Electron dose: 31.78 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 5379
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansMovie frames/image: 40

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4CTFFINDCTF correction
10SPHIREinitial Euler assignment
11SPARXfinal Euler assignment
12SPARXclassification
13SPARX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 208206
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208206 / Symmetry type: POINT

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