6SWA

Mus musculus brain neocortex ribosome 60S bound to Ebp1

  • Classification: RIBOSOME
  • Organism(s): Mus musculus
  • Mutation(s): No 

  • Deposited: 2019-09-20 Released: 2020-09-30 
  • Deposition Author(s): Kraushar, M.L., Sprink, T.
  • Funding Organization(s): European Molecular Biology Organization (EMBO), Alexander von Humboldt Foundation, European Union (EU)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit.

Kraushar, M.L., Krupp, F., Harnett, D., Turko, P., Ambrozkiewicz, M.C., Sprink, T., Imami, K., Gunnigmann, M., Zinnall, U., Vieira-Vieira, C.H., Schaub, T., Munster-Wandowski, A., Burger, J., Borisova, E., Yamamoto, H., Rasin, M.R., Ohler, U., Beule, D., Mielke, T., Tarabykin, V., Landthaler, M., Kramer, G., Vida, I., Selbach, M., Spahn, C.M.T.

(2021) Mol Cell 81: 304

  • DOI: 10.1016/j.molcel.2020.11.037
  • Primary Citation of Related Structures:  
    6SWA

  • PubMed 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 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) ...

    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.

    Organizational Affiliation: 

    Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany. Electronic address: christian.spahn@charite.de.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8 A252Mus musculusMutation(s): 0 
Gene Names: Rpl8
Find proteins for P62918 (Mus musculus)
Explore P62918 
Go to UniProtKB:  P62918
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3 B394Mus musculusMutation(s): 0 
Gene Names: Rpl3
Find proteins for P27659 (Mus musculus)
Explore P27659 
Go to UniProtKB:  P27659
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4 C363Mus musculusMutation(s): 0 
Gene Names: Rpl4
Find proteins for Q9D8E6 (Mus musculus)
Explore Q9D8E6 
Go to UniProtKB:  Q9D8E6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5 D294Mus musculusMutation(s): 0 
Gene Names: Rpl5
Find proteins for P47962 (Mus musculus)
Explore P47962 
Go to UniProtKB:  P47962
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6 E194Mus musculusMutation(s): 0 
Gene Names: Rpl6
Find proteins for P47911 (Mus musculus)
Explore P47911 
Go to UniProtKB:  P47911
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7 F234Mus musculusMutation(s): 0 
Gene Names: Rpl7
Find proteins for P14148 (Mus musculus)
Explore P14148 
Go to UniProtKB:  P14148
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7a G234Mus musculusMutation(s): 0 
Gene Names: Rpl7a, Surf-3, Surf3
Find proteins for P12970 (Mus musculus)
Explore P12970 
Go to UniProtKB:  P12970
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9 H191Mus musculusMutation(s): 0 
Gene Names: Rpl9
Find proteins for P51410 (Mus musculus)
Explore P51410 
Go to UniProtKB:  P51410
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10 I211Mus musculusMutation(s): 0 
Gene Names: Rpl10, Qm
Find proteins for Q6ZWV3 (Mus musculus)
Explore Q6ZWV3 
Go to UniProtKB:  Q6ZWV3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11 J169Mus musculusMutation(s): 0 
Gene Names: Rpl11
Find proteins for Q9CXW4 (Mus musculus)
Explore Q9CXW4 
Go to UniProtKB:  Q9CXW4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13 K205Mus musculusMutation(s): 0 
Gene Names: Rpl13
Find proteins for P47963 (Mus musculus)
Explore P47963 
Go to UniProtKB:  P47963
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14 L139Mus musculusMutation(s): 0 
Gene Names: Rpl14
Find proteins for Q9CR57 (Mus musculus)
Explore Q9CR57 
Go to UniProtKB:  Q9CR57
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15 M203Mus musculusMutation(s): 0 
Gene Names: Rpl15
Find proteins for Q9CZM2 (Mus musculus)
Explore Q9CZM2 
Go to UniProtKB:  Q9CZM2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13a N195Mus musculusMutation(s): 0 
Gene Names: Rpl13a, P198, Tstap198-7
Find proteins for P19253 (Mus musculus)
Explore P19253 
Go to UniProtKB:  P19253
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17 O153Mus musculusMutation(s): 0 
Gene Names: Rpl17
Find proteins for Q9CPR4 (Mus musculus)
Explore Q9CPR4 
Go to UniProtKB:  Q9CPR4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18 P185Mus musculusMutation(s): 0 
Gene Names: Rpl18
Find proteins for P35980 (Mus musculus)
Explore P35980 
Go to UniProtKB:  P35980
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18a Q175Mus musculusMutation(s): 0 
Gene Names: Rpl18a
Find proteins for P62717 (Mus musculus)
Explore P62717 
Go to UniProtKB:  P62717
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21 R157Mus musculusMutation(s): 0 
Gene Names: Rpl21
Find proteins for O09167 (Mus musculus)
Explore O09167 
Go to UniProtKB:  O09167
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22 S101Mus musculusMutation(s): 0 
Gene Names: Rpl22
Find proteins for P67984 (Mus musculus)
Explore P67984 
Go to UniProtKB:  P67984
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23 T129Mus musculusMutation(s): 0 
Gene Names: Rpl23
Find proteins for P62830 (Mus musculus)
Explore P62830 
Go to UniProtKB:  P62830
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24 U62Mus musculusMutation(s): 0 
Gene Names: Rpl24
Find proteins for Q8BP67 (Mus musculus)
Explore Q8BP67 
Go to UniProtKB:  Q8BP67
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23a V118Mus musculusMutation(s): 0 
Gene Names: Rpl23a
Find proteins for P62751 (Mus musculus)
Explore P62751 
Go to UniProtKB:  P62751
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L26 W127Mus musculusMutation(s): 0 
Gene Names: Rpl26
Find proteins for Q4FZH2 (Mus musculus)
Explore Q4FZH2 
Go to UniProtKB:  Q4FZH2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27 X134Mus musculusMutation(s): 0 
Gene Names: Rpl27
Find proteins for Q5BLJ9 (Mus musculus)
Explore Q5BLJ9 
Go to UniProtKB:  Q5BLJ9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27a Y147Mus musculusMutation(s): 0 
Gene Names: Rpl27a
Find proteins for P14115 (Mus musculus)
Explore P14115 
Go to UniProtKB:  P14115
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29 Z68Mus musculusMutation(s): 0 
Gene Names: Rpl29, Rpl43
Find proteins for P47915 (Mus musculus)
Explore P47915 
Go to UniProtKB:  P47915
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30 a97Mus musculusMutation(s): 0 
Gene Names: Rpl30
Find proteins for P62889 (Mus musculus)
Explore P62889 
Go to UniProtKB:  P62889
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31 b106Mus musculusMutation(s): 0 
Gene Names: Rpl31
Find proteins for P62900 (Mus musculus)
Explore P62900 
Go to UniProtKB:  P62900
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32 c129Mus musculusMutation(s): 0 
Gene Names: Rpl32
Find proteins for P62911 (Mus musculus)
Explore P62911 
Go to UniProtKB:  P62911
NIH Common Fund Data Resources
IMPC:  MGI:98038
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35a d109Mus musculusMutation(s): 0 
Gene Names: Rpl35a
Find proteins for O55142 (Mus musculus)
Explore O55142 
Go to UniProtKB:  O55142
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34 e114Mus musculusMutation(s): 0 
Gene Names: Rpl34
Find proteins for Q9D1R9 (Mus musculus)
Explore Q9D1R9 
Go to UniProtKB:  Q9D1R9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35 f122Mus musculusMutation(s): 0 
Gene Names: Rpl35
Find proteins for Q6ZWV7 (Mus musculus)
Explore Q6ZWV7 
Go to UniProtKB:  Q6ZWV7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36 g98Mus musculusMutation(s): 0 
Gene Names: Rpl36
Find proteins for P47964 (Mus musculus)
Explore P47964 
Go to UniProtKB:  P47964
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37 h84Mus musculusMutation(s): 0 
Gene Names: Rpl37
Find proteins for Q9D823 (Mus musculus)
Explore Q9D823 
Go to UniProtKB:  Q9D823
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38 i69Mus musculusMutation(s): 0 
Gene Names: Rpl38
Find proteins for Q9JJI8 (Mus musculus)
Explore Q9JJI8 
Go to UniProtKB:  Q9JJI8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L39 j50Mus musculusMutation(s): 0 
Gene Names: Rpl39
Find proteins for Q505A8 (Mus musculus)
Explore Q505A8 
Go to UniProtKB:  Q505A8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L40 k50Mus musculusMutation(s): 0 
Gene Names: Uba52
Find proteins for Q5M9K3 (Mus musculus)
Explore Q5M9K3 
Go to UniProtKB:  Q5M9K3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41 l25Mus musculusMutation(s): 0 
Gene Names: Rpl41
Find proteins for P62947 (Mus musculus)
Explore P62947 
Go to UniProtKB:  P62947
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L36A m105Mus musculusMutation(s): 0 
Gene Names: Rpl36a
Find proteins for Q5M9P1 (Mus musculus)
Explore Q5M9P1 
Go to UniProtKB:  Q5M9P1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L37a n91Mus musculusMutation(s): 0 
Gene Names: Rpl37a
Find proteins for Q4VAF2 (Mus musculus)
Explore Q4VAF2 
Go to UniProtKB:  Q4VAF2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19 o184Mus musculusMutation(s): 0 
Gene Names: Rpl19
Find proteins for P84099 (Mus musculus)
Explore P84099 
Go to UniProtKB:  P84099
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28 p122Mus musculusMutation(s): 0 
Gene Names: Rpl28
Find proteins for P41105 (Mus musculus)
Explore P41105 
Go to UniProtKB:  P41105
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4 t353Mus musculusMutation(s): 0 
Gene Names: Pa2g4, Ebp1, Plfap
Find proteins for P50580 (Mus musculus)
Explore P50580 
Go to UniProtKB:  P50580
NIH Common Fund Data Resources
IMPC:  MGI:894684
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 43
MoleculeChainsLengthOrganismImage
28S ribosomal RNAq3612Mus musculus
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 44
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAr157Mus musculus
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 45
MoleculeChainsLengthOrganismImage
5S ribosomal RNAs119Mus musculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
h, m, n
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B, K, M, P, W, b, c, l, q, r, s
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)Germany190-2016
Alexander von Humboldt FoundationGermany--
European Union (EU)GermanyiNEXT (PID: 2227)
European Union (EU)GermanyInstruct-ERIC Pilot R&D Project (APPID: 232)

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 2.0: 2021-02-17
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary