7Y7E

Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.

Zhao, X.Ma, D.Ishiguro, K.Saito, H.Akichika, S.Matsuzawa, I.Mito, M.Irie, T.Ishibashi, K.Wakabayashi, K.Sakaguchi, Y.Yokoyama, T.Mishima, Y.Shirouzu, M.Iwasaki, S.Suzuki, T.Suzuki, T.

(2023) Cell 186: 5517

  • DOI: https://doi.org/10.1016/j.cell.2023.10.026
  • Primary Citation of Related Structures:  
    7Y7C, 7Y7D, 7Y7E, 7Y7F, 7Y7G, 7Y7H, 8JDJ, 8JDK, 8JDL, 8JDM

  • PubMed Abstract: 

    Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.


  • Organizational Affiliation

    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2241Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, fully modified isoform135Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7179Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9130Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10103Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13118Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14101Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1589Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1682Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1784Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1875Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1992Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2087Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2171Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth c]273Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Y [auth d]209Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4Z [auth e]201Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth f]179Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth g]177Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9CA [auth h]149Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13DA [auth i]142Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14EA [auth j]123Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15FA [auth k]144Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16GA [auth l]136Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17HA [auth m]127Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18IA [auth n]117Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19JA [auth o]115Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20KA [auth p]118Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21LA [auth q]103Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22MA [auth r]110Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23NA [auth s]100Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24OA [auth t]104Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25PA [auth u]94Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27QA [auth v]85Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28RA [auth w]78Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29SA [auth x]63Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30TA [auth y]59Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32UA [auth z]57Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33VA [auth 0]55Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34WA [auth 1]46Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35XA [auth 2]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Q1
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UniProt GroupP0A7Q1
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36YA [auth 3]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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UniProt GroupP0A7Q6
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31ZA [auth 4]70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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UniProt GroupP0A7M9
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
23S rRNAV [auth a]2,904Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
5S rRNAW [auth b]120Escherichia coli
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth X]35Escherichia coli
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Entity ID: 54
MoleculeChains LengthOrganismImage
P-site tRNA-fMetBB [auth Z]77Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
A-site tRNA-AspCB [auth V]75Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
RK [auth V]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth a]
AF [auth a]
AG [auth a]
AC [auth A],
AD [auth A],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth a],
AI [auth a],
AJ [auth a],
AK [auth a],
BC [auth A],
BD [auth A],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth a],
BI [auth a],
BJ [auth a],
BK [auth a],
CC [auth A],
CD [auth A],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth a],
CJ [auth a],
CK [auth a],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth a],
DI [auth a],
DJ [auth a],
DK [auth a],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth a],
EF [auth a],
EG [auth a],
EH [auth a],
EI [auth a],
EJ [auth a],
EK [auth a],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FI [auth a],
FJ [auth a],
FK [auth a],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth a],
GF [auth a],
GG [auth a],
GH [auth a],
GI [auth a],
GJ [auth a],
GK [auth b],
HB [auth A],
HC [auth A],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth a],
HH [auth a],
HI [auth a],
HJ [auth a],
HK [auth b],
IB [auth A],
IC [auth A],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth a],
IH [auth a],
II [auth a],
IJ [auth a],
IK [auth b],
JB [auth A],
JC [auth A],
JD [auth a],
JE [auth a],
JF [auth a],
JG [auth a],
JH [auth a],
JI [auth a],
JJ [auth a],
JK [auth c],
KB [auth A],
KC [auth A],
KD [auth a],
KE [auth a],
KF [auth a],
KG [auth a],
KH [auth a],
KI [auth a],
KJ [auth a],
KK [auth d],
LB [auth A],
LC [auth A],
LD [auth a],
LE [auth a],
LF [auth a],
LG [auth a],
LH [auth a],
LI [auth a],
LJ [auth a],
LK [auth z],
MB [auth A],
MC [auth A],
MD [auth a],
ME [auth a],
MF [auth a],
MG [auth a],
MH [auth a],
MI [auth a],
MJ [auth a],
MK [auth Z],
NB [auth A],
NC [auth A],
ND [auth a],
NE [auth a],
NF [auth a],
NG [auth a],
NH [auth a],
NI [auth a],
NJ [auth a],
NK [auth Z],
OB [auth A],
OC [auth A],
OD [auth a],
OE [auth a],
OF [auth a],
OG [auth a],
OH [auth a],
OI [auth a],
OJ [auth a],
OK [auth Z],
PB [auth A],
PC [auth A],
PD [auth a],
PE [auth a],
PF [auth a],
PG [auth a],
PH [auth a],
PI [auth a],
PJ [auth a],
PK [auth V],
QB [auth A],
QC [auth A],
QD [auth a],
QE [auth a],
QF [auth a],
QG [auth a],
QH [auth a],
QI [auth a],
QJ [auth a],
QK [auth V],
RB [auth A],
RC [auth A],
RD [auth a],
RE [auth a],
RF [auth a],
RG [auth a],
RH [auth a],
RI [auth a],
RJ [auth a],
SB [auth A],
SC [auth A],
SD [auth a],
SE [auth a],
SF [auth a],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
TB [auth A],
TC [auth A],
TD [auth a],
TE [auth a],
TF [auth a],
TG [auth a],
TH [auth a],
TI [auth a],
TJ [auth a],
UB [auth A],
UC [auth A],
UD [auth a],
UE [auth a],
UF [auth a],
UG [auth a],
UH [auth a],
UI [auth a],
UJ [auth a],
VB [auth A],
VC [auth A],
VD [auth a],
VE [auth a],
VF [auth a],
VG [auth a],
VH [auth a],
VI [auth a],
VJ [auth a],
WB [auth A],
WC [auth A],
WD [auth a],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth a],
WI [auth a],
WJ [auth a],
XB [auth A],
XC [auth A],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth a],
XI [auth a],
XJ [auth a],
YB [auth A],
YC [auth A],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth a],
YI [auth a],
YJ [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth a],
ZI [auth a],
ZJ [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
Y [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
GA [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
MODEL REFINEMENTCoot0.9.5
RECONSTRUCTIONRELION3.1.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--
Japan Society for the Promotion of Science (JSPS)Japan26113003, 26220205 and 18H05272
Japan Science and TechnologyJapanJPMJER2002

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-12-06
    Changes: Database references
  • Version 2.2: 2023-12-27
    Changes: Database references