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: https://doi.org/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). 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: matthew.kraushar@molgen.mpg.de.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8252Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3394Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4363Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5294Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6194Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7234Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7a234Mus musculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9191Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10211Mus musculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11169Mus musculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13205Mus musculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14139Mus musculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15203Mus musculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13a195Mus musculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17153Mus musculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18185Mus musculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18a175Mus musculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21157Mus musculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22101Mus musculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23129Mus musculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2462Mus musculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23a118Mus musculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26127Mus musculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27134Mus musculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27a147Mus musculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2968Mus musculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30AA [auth a]97Mus musculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31BA [auth b]106Mus musculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32CA [auth c]129Mus musculusMutation(s): 0 
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IMPC:  MGI:98038
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aDA [auth d]109Mus musculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34EA [auth e]114Mus musculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35FA [auth f]122Mus musculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36GA [auth g]98Mus musculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37HA [auth h]84Mus musculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38IA [auth i]69Mus musculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39JA [auth j]50Mus musculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40KA [auth k]50Mus musculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41LA [auth l]25Mus musculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36AMA [auth m]105Mus musculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37aNA [auth n]91Mus musculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19OA [auth o]184Mus musculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28PA [auth p]122Mus musculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4TA [auth t]353Mus musculusMutation(s): 0 
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IMPC:  MGI:894684
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Entity ID: 43
MoleculeChains LengthOrganismImage
28S ribosomal RNAQA [auth q]3,612Mus musculus
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Entity ID: 44
MoleculeChains LengthOrganismImage
5.8S ribosomal RNARA [auth r]157Mus musculus
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Entity ID: 45
MoleculeChains LengthOrganismImage
5S ribosomal RNASA [auth s]119Mus musculus
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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BB [auth h],
DB [auth m],
EB [auth n]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth c]
AC [auth q]
AD [auth q]
AE [auth q]
AF [auth q]
AB [auth c],
AC [auth q],
AD [auth q],
AE [auth q],
AF [auth q],
AG [auth q],
AH [auth q],
AI [auth q],
AJ [auth q],
AK [auth r],
BC [auth q],
BD [auth q],
BE [auth q],
BF [auth q],
BG [auth q],
BH [auth q],
BI [auth q],
BJ [auth q],
BK [auth s],
CB [auth l],
CC [auth q],
CD [auth q],
CE [auth q],
CF [auth q],
CG [auth q],
CH [auth q],
CI [auth q],
CJ [auth q],
CK [auth s],
DC [auth q],
DD [auth q],
DE [auth q],
DF [auth q],
DG [auth q],
DH [auth q],
DI [auth q],
DJ [auth q],
DK [auth s],
EC [auth q],
ED [auth q],
EE [auth q],
EF [auth q],
EG [auth q],
EH [auth q],
EI [auth q],
EJ [auth q],
EK [auth s],
FB [auth q],
FC [auth q],
FD [auth q],
FE [auth q],
FF [auth q],
FG [auth q],
FH [auth q],
FI [auth q],
FJ [auth q],
FK [auth s],
GB [auth q],
GC [auth q],
GD [auth q],
GE [auth q],
GF [auth q],
GG [auth q],
GH [auth q],
GI [auth q],
GJ [auth q],
GK [auth s],
HB [auth q],
HC [auth q],
HD [auth q],
HE [auth q],
HF [auth q],
HG [auth q],
HH [auth q],
HI [auth q],
HJ [auth q],
HK [auth s],
IB [auth q],
IC [auth q],
ID [auth q],
IE [auth q],
IF [auth q],
IG [auth q],
IH [auth q],
II [auth q],
IJ [auth q],
IK [auth s],
JB [auth q],
JC [auth q],
JD [auth q],
JE [auth q],
JF [auth q],
JG [auth q],
JH [auth q],
JI [auth q],
JJ [auth q],
JK [auth s],
KB [auth q],
KC [auth q],
KD [auth q],
KE [auth q],
KF [auth q],
KG [auth q],
KH [auth q],
KI [auth q],
KJ [auth q],
LB [auth q],
LC [auth q],
LD [auth q],
LE [auth q],
LF [auth q],
LG [auth q],
LH [auth q],
LI [auth q],
LJ [auth q],
MB [auth q],
MC [auth q],
MD [auth q],
ME [auth q],
MF [auth q],
MG [auth q],
MH [auth q],
MI [auth q],
MJ [auth q],
NB [auth q],
NC [auth q],
ND [auth q],
NE [auth q],
NF [auth q],
NG [auth q],
NH [auth q],
NI [auth q],
NJ [auth q],
OB [auth q],
OC [auth q],
OD [auth q],
OE [auth q],
OF [auth q],
OG [auth q],
OH [auth q],
OI [auth q],
OJ [auth q],
PB [auth q],
PC [auth q],
PD [auth q],
PE [auth q],
PF [auth q],
PG [auth q],
PH [auth q],
PI [auth q],
PJ [auth q],
QB [auth q],
QC [auth q],
QD [auth q],
QE [auth q],
QF [auth q],
QG [auth q],
QH [auth q],
QI [auth q],
QJ [auth q],
RB [auth q],
RC [auth q],
RD [auth q],
RE [auth q],
RF [auth q],
RG [auth q],
RH [auth q],
RI [auth q],
RJ [auth q],
SB [auth q],
SC [auth q],
SD [auth q],
SE [auth q],
SF [auth q],
SG [auth q],
SH [auth q],
SI [auth q],
SJ [auth q],
TB [auth q],
TC [auth q],
TD [auth q],
TE [auth q],
TF [auth q],
TG [auth q],
TH [auth q],
TI [auth q],
TJ [auth q],
UA [auth B],
UB [auth q],
UC [auth q],
UD [auth q],
UE [auth q],
UF [auth q],
UG [auth q],
UH [auth q],
UI [auth q],
UJ [auth r],
VA [auth K],
VB [auth q],
VC [auth q],
VD [auth q],
VE [auth q],
VF [auth q],
VG [auth q],
VH [auth q],
VI [auth q],
VJ [auth r],
WA [auth M],
WB [auth q],
WC [auth q],
WD [auth q],
WE [auth q],
WF [auth q],
WG [auth q],
WH [auth q],
WI [auth q],
WJ [auth r],
XA [auth P],
XB [auth q],
XC [auth q],
XD [auth q],
XE [auth q],
XF [auth q],
XG [auth q],
XH [auth q],
XI [auth q],
XJ [auth r],
YA [auth W],
YB [auth q],
YC [auth q],
YD [auth q],
YE [auth q],
YF [auth q],
YG [auth q],
YH [auth q],
YI [auth q],
YJ [auth r],
ZA [auth b],
ZB [auth q],
ZC [auth q],
ZD [auth q],
ZE [auth q],
ZF [auth q],
ZG [auth q],
ZH [auth q],
ZI [auth q],
ZJ [auth r]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPARX

Structure Validation

View Full Validation Report



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