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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8 A252Mus musculusMutation(s): 0 
Gene Names: Rpl8
Find proteins for P62918 (Mus musculus)
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Entity ID: 2
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60S ribosomal protein L3 B394Mus musculusMutation(s): 0 
Gene Names: Rpl3
Find proteins for P27659 (Mus musculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4 C363Mus musculusMutation(s): 0 
Gene Names: Rpl4
Find proteins for Q9D8E6 (Mus musculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5 D294Mus musculusMutation(s): 0 
Gene Names: Rpl5
Find proteins for P47962 (Mus musculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6 E194Mus musculusMutation(s): 0 
Gene Names: Rpl6
Find proteins for P47911 (Mus musculus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7 F234Mus musculusMutation(s): 0 
Gene Names: Rpl7
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7a G234Mus musculusMutation(s): 0 
Gene Names: Rpl7aSurf-3Surf3
Find proteins for P12970 (Mus musculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9 H191Mus musculusMutation(s): 0 
Gene Names: Rpl9
Find proteins for P51410 (Mus musculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10 I211Mus musculusMutation(s): 0 
Gene Names: Rpl10Qm
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Entity ID: 10
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60S ribosomal protein L11 J169Mus musculusMutation(s): 0 
Gene Names: Rpl11
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Entity ID: 11
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60S ribosomal protein L13 K205Mus musculusMutation(s): 0 
Gene Names: Rpl13
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Entity ID: 12
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60S ribosomal protein L14 L139Mus musculusMutation(s): 0 
Gene Names: Rpl14
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Entity ID: 13
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60S ribosomal protein L15 M203Mus musculusMutation(s): 0 
Gene Names: Rpl15
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Entity ID: 14
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60S ribosomal protein L13a N195Mus musculusMutation(s): 0 
Gene Names: Rpl13aP198Tstap198-7
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Entity ID: 15
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60S ribosomal protein L17 O153Mus musculusMutation(s): 0 
Gene Names: Rpl17
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18 P185Mus musculusMutation(s): 0 
Gene Names: Rpl18
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Entity ID: 17
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60S ribosomal protein L18a Q175Mus musculusMutation(s): 0 
Gene Names: Rpl18a
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Entity ID: 18
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60S ribosomal protein L21 R157Mus musculusMutation(s): 0 
Gene Names: Rpl21
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Entity ID: 19
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60S ribosomal protein L22 S101Mus musculusMutation(s): 0 
Gene Names: Rpl22
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Entity ID: 20
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60S ribosomal protein L23 T129Mus musculusMutation(s): 0 
Gene Names: Rpl23
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Entity ID: 21
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60S ribosomal protein L24 U62Mus musculusMutation(s): 0 
Gene Names: Rpl24
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Entity ID: 22
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60S ribosomal protein L23a V118Mus musculusMutation(s): 0 
Gene Names: Rpl23a
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Entity ID: 23
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Ribosomal protein L26 W127Mus musculusMutation(s): 0 
Gene Names: Rpl26
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Entity ID: 24
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60S ribosomal protein L27 X134Mus musculusMutation(s): 0 
Gene Names: Rpl27
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Entity ID: 25
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60S ribosomal protein L27a Y147Mus musculusMutation(s): 0 
Gene Names: Rpl27a
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Entity ID: 26
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60S ribosomal protein L29 Z68Mus musculusMutation(s): 0 
Gene Names: Rpl29Rpl43
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Entity ID: 27
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60S ribosomal protein L30 a97Mus musculusMutation(s): 0 
Gene Names: Rpl30
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Entity ID: 28
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60S ribosomal protein L31 b106Mus musculusMutation(s): 0 
Gene Names: Rpl31
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Entity ID: 29
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60S ribosomal protein L32 c129Mus musculusMutation(s): 0 
Gene Names: Rpl32
Find proteins for P62911 (Mus musculus)
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NIH Common Fund Data Resources
IMPC:  MGI:98038
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Entity ID: 30
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60S ribosomal protein L35a d109Mus musculusMutation(s): 0 
Gene Names: Rpl35a
Find proteins for O55142 (Mus musculus)
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Entity ID: 31
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60S ribosomal protein L34 e114Mus musculusMutation(s): 0 
Gene Names: Rpl34
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Entity ID: 32
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60S ribosomal protein L35 f122Mus musculusMutation(s): 0 
Gene Names: Rpl35
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Entity ID: 33
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60S ribosomal protein L36 g98Mus musculusMutation(s): 0 
Gene Names: Rpl36
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Entity ID: 34
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60S ribosomal protein L37 h84Mus musculusMutation(s): 0 
Gene Names: Rpl37
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Entity ID: 35
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60S ribosomal protein L38 i69Mus musculusMutation(s): 0 
Gene Names: Rpl38
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Entity ID: 36
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Ribosomal protein L39 j50Mus musculusMutation(s): 0 
Gene Names: Rpl39
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Entity ID: 37
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60S ribosomal protein L40 k50Mus musculusMutation(s): 0 
Gene Names: Uba52
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Entity ID: 38
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60S ribosomal protein L41 l25Mus musculusMutation(s): 0 
Gene Names: Rpl41
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Entity ID: 39
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Ribosomal protein L36A m105Mus musculusMutation(s): 0 
Gene Names: Rpl36a
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Entity ID: 40
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Ribosomal protein L37a n91Mus musculusMutation(s): 0 
Gene Names: Rpl37a
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Entity ID: 41
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60S ribosomal protein L19 o184Mus musculusMutation(s): 0 
Gene Names: Rpl19
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Entity ID: 42
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60S ribosomal protein L28 p122Mus musculusMutation(s): 0 
Gene Names: Rpl28
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Entity ID: 46
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Proliferation-associated protein 2G4 t353Mus musculusMutation(s): 0 
Gene Names: Pa2g4Ebp1Plfap
Find proteins for P50580 (Mus musculus)
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IMPC:  MGI:894684
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Entity ID: 43
MoleculeChainsLengthOrganismImage
28S ribosomal RNAq3612Mus musculus
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Entity ID: 44
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAr157Mus musculus
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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

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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