8BPO

Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of ribosome-associated mRNA degradation during tubulin autoregulation.

Hopfler, M.Absmeier, E.Peak-Chew, S.Y.Vartholomaiou, E.Passmore, L.A.Gasic, I.Hegde, R.S.

(2023) Mol Cell 83: 2290

  • DOI: https://doi.org/10.1016/j.molcel.2023.05.020
  • Primary Citation of Related Structures:  
    8BPO

  • PubMed Abstract: 

    Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits affects polymerization dynamics and microtubule function. When cells sense excess free tubulin, they trigger degradation of the encoding mRNAs, which requires recognition of the nascent polypeptide by the tubulin-specific ribosome-binding factor TTC5. How TTC5 initiates the decay of tubulin mRNAs is unknown. Here, our biochemical and structural analysis reveals that TTC5 recruits the poorly studied protein SCAPER to the ribosome. SCAPER, in turn, engages the CCR4-NOT deadenylase complex through its CNOT11 subunit to trigger tubulin mRNA decay. SCAPER mutants that cause intellectual disability and retinitis pigmentosa in humans are impaired in CCR4-NOT recruitment, tubulin mRNA degradation, and microtubule-dependent chromosome segregation. Our findings demonstrate how recognition of a nascent polypeptide on the ribosome is physically linked to mRNA decay factors via a relay of protein-protein interactions, providing a paradigm for specificity in cytoplasmic gene regulation.


  • Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent polypeptide-associated complex subunit alpha N-terminal regionD [auth D1]29Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth A2]257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3F [auth B2]403Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4G [auth C2]425Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18_c domain-containing proteinH [auth D2]297Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth E2]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7J [auth F2]247Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aK [auth G2]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9L [auth H2]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10M [auth I2]214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11N [auth J2]178Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13O [auth K2]211Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TKB3 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14P [auth L2]218Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth M2]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aR [auth N2]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17S [auth O2]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18T [auth P2]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19U [auth Q2]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aV [auth R2]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21W [auth S2]160Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22X [auth T2]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23Y [auth U2]140Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth V2]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L23eN domain-containing proteinAA [auth W2]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26BA [auth X2]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27CA [auth Y2]136Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aDA [auth Z2]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth a2]226Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30FA [auth b2]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31GA [auth c2]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32HA [auth d2]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aIA [auth e2]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34JA [auth f2]116Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35KA [auth g2]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36LA [auth h2]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37MA [auth i2]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38NA [auth j2]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-likeOA [auth k2]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40PA [auth l2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41QA [auth m2]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36a-likeRA [auth n2]106Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aSA [auth o2]92Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28TA [auth p2]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0UA [auth q2]318Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12VA [auth r2]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
S phase cyclin A-associated protein in the endoplasmic reticulumWA [auth s2]1,411Homo sapiensMutation(s): 0 
Gene Names: SCAPERKIAA1454ZNF291MSTP063
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GTEx:  ENSG00000140386 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Tetratricopeptide repeat protein 5XA [auth t2]489Homo sapiensMutation(s): 0 
Gene Names: TTC5
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GTEx:  ENSG00000136319 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chainYA [auth u2]64Homo sapiensMutation(s): 0 
Gene Names: TUBBTUBB5OK/SW-cl.56
UniProt & NIH Common Fund Data Resources
Find proteins for P07437 (Homo sapiens)
Explore P07437 
Go to UniProtKB:  P07437
PHAROS:  P07437
GTEx:  ENSG00000196230 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07437
Sequence Annotations
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S ribosomal RNAA [auth A1]4,380Oryctolagus cuniculus
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth B1]120Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAC [auth C1]156Oryctolagus cuniculus
Sequence Annotations
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EJ [auth f2],
GJ [auth i2],
HJ [auth l2],
IJ [auth n2],
JJ [auth o2]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A1]
AC [auth A1]
AD [auth A1]
AE [auth A1]
AF [auth A1]
AB [auth A1],
AC [auth A1],
AD [auth A1],
AE [auth A1],
AF [auth A1],
AG [auth A1],
AH [auth A1],
AI [auth A1],
AJ [auth O2],
BB [auth A1],
BC [auth A1],
BD [auth A1],
BE [auth A1],
BF [auth A1],
BG [auth A1],
BH [auth A1],
BI [auth A1],
BJ [auth O2],
CB [auth A1],
CC [auth A1],
CD [auth A1],
CE [auth A1],
CF [auth A1],
CG [auth A1],
CH [auth A1],
CI [auth A1],
CJ [auth U2],
DB [auth A1],
DC [auth A1],
DD [auth A1],
DE [auth A1],
DF [auth A1],
DG [auth A1],
DH [auth A1],
DI [auth A1],
DJ [auth Z2],
EB [auth A1],
EC [auth A1],
ED [auth A1],
EE [auth A1],
EF [auth A1],
EG [auth A1],
EH [auth A1],
EI [auth A1],
FB [auth A1],
FC [auth A1],
FD [auth A1],
FE [auth A1],
FF [auth A1],
FG [auth A1],
FH [auth A1],
FI [auth A1],
FJ [auth f2],
GB [auth A1],
GC [auth A1],
GD [auth A1],
GE [auth A1],
GF [auth A1],
GG [auth A1],
GH [auth A1],
GI [auth A1],
HB [auth A1],
HC [auth A1],
HD [auth A1],
HE [auth A1],
HF [auth A1],
HG [auth A1],
HH [auth A1],
HI [auth A1],
IB [auth A1],
IC [auth A1],
ID [auth A1],
IE [auth A1],
IF [auth A1],
IG [auth A1],
IH [auth A1],
II [auth A1],
JB [auth A1],
JC [auth A1],
JD [auth A1],
JE [auth A1],
JF [auth A1],
JG [auth A1],
JH [auth A1],
JI [auth A1],
KB [auth A1],
KC [auth A1],
KD [auth A1],
KE [auth A1],
KF [auth A1],
KG [auth A1],
KH [auth A1],
KI [auth A1],
LB [auth A1],
LC [auth A1],
LD [auth A1],
LE [auth A1],
LF [auth A1],
LG [auth A1],
LH [auth A1],
LI [auth B1],
MB [auth A1],
MC [auth A1],
MD [auth A1],
ME [auth A1],
MF [auth A1],
MG [auth A1],
MH [auth A1],
MI [auth B1],
NB [auth A1],
NC [auth A1],
ND [auth A1],
NE [auth A1],
NF [auth A1],
NG [auth A1],
NH [auth A1],
NI [auth B1],
OB [auth A1],
OC [auth A1],
OD [auth A1],
OE [auth A1],
OF [auth A1],
OG [auth A1],
OH [auth A1],
OI [auth B1],
PB [auth A1],
PC [auth A1],
PD [auth A1],
PE [auth A1],
PF [auth A1],
PG [auth A1],
PH [auth A1],
PI [auth B1],
QB [auth A1],
QC [auth A1],
QD [auth A1],
QE [auth A1],
QF [auth A1],
QG [auth A1],
QH [auth A1],
QI [auth B1],
RB [auth A1],
RC [auth A1],
RD [auth A1],
RE [auth A1],
RF [auth A1],
RG [auth A1],
RH [auth A1],
RI [auth B1],
SB [auth A1],
SC [auth A1],
SD [auth A1],
SE [auth A1],
SF [auth A1],
SG [auth A1],
SH [auth A1],
SI [auth C1],
TB [auth A1],
TC [auth A1],
TD [auth A1],
TE [auth A1],
TF [auth A1],
TG [auth A1],
TH [auth A1],
TI [auth C1],
UB [auth A1],
UC [auth A1],
UD [auth A1],
UE [auth A1],
UF [auth A1],
UG [auth A1],
UH [auth A1],
UI [auth C1],
VB [auth A1],
VC [auth A1],
VD [auth A1],
VE [auth A1],
VF [auth A1],
VG [auth A1],
VH [auth A1],
VI [auth C1],
WB [auth A1],
WC [auth A1],
WD [auth A1],
WE [auth A1],
WF [auth A1],
WG [auth A1],
WH [auth A1],
WI [auth C1],
XB [auth A1],
XC [auth A1],
XD [auth A1],
XE [auth A1],
XF [auth A1],
XG [auth A1],
XH [auth A1],
XI [auth C1],
YB [auth A1],
YC [auth A1],
YD [auth A1],
YE [auth A1],
YF [auth A1],
YG [auth A1],
YH [auth A1],
YI [auth B2],
ZA [auth A1],
ZB [auth A1],
ZC [auth A1],
ZD [auth A1],
ZE [auth A1],
ZF [auth A1],
ZG [auth A1],
ZH [auth A1],
ZI [auth I2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_A022_1007
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105192715
European Molecular Biology Organization (EMBO)European UnionALTF 116-2020
H2020 Marie Curie Actions of the European CommissionEuropean Union101029853
German Research Foundation (DFG)Germany429892960
Swiss National Science FoundationSwitzerlandPCEFP3_194312
Damon Runyon Cancer Research FoundationUnited StatesDRG:2279-16

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references