4X66

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics.

Choi, J., Ieong, K.W., Demirci, H., Chen, J., Petrov, A., Prabhakar, A., O'Leary, S.E., Dominissini, D., Rechavi, G., Soltis, S.M., Ehrenberg, M., Puglisi, J.D.

(2016) Nat Struct Mol Biol 23: 110-115

  • DOI: https://doi.org/10.1038/nsmb.3148
  • Primary Citation of Related Structures:  
    4X62, 4X64, 4X65, 4X66

  • PubMed Abstract: 

    N(6)-methylation of adenosine (forming m(6)A) is the most abundant post-transcriptional modification within the coding region of mRNA, but its role during translation remains unknown. Here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)A in mRNA decoding. Although m(6)A base-pairs with uridine during decoding, as shown by X-ray crystallographic analyses of Thermus thermophilus ribosomal complexes, our measurements in an Escherichia coli translation system revealed that m(6)A modification of mRNA acts as a barrier to tRNA accommodation and translation elongation. The interaction between an m(6)A-modified codon and cognate tRNA echoes the interaction between a near-cognate codon and tRNA, because delay in tRNA accommodation depends on the position and context of m(6)A within codons and on the accuracy level of translation. Overall, our results demonstrate that chemical modification of mRNA can change translational dynamics.

    • Organizational Affiliation: 

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2236Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3207Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5151Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7155Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9127Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1099Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11119Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12125Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1588Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1684Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1799Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1873Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1981Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2099Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein Thx25Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
RNA (5'-D(*AP*AP*(MA6)P*UP*UP*U)-3')V [auth a]6Thermus thermophilus HB8
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Entity ID: 23
MoleculeChains LengthOrganismImage
RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')W [auth b]11Thermus thermophilus HB8
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR
Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
X [auth A]
Y [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
X [auth A],
Y [auth A],
Z [auth A]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BN [auth N],
QM [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
AL [auth A]
AM [auth A]
BL [auth A]
BM [auth A]
CL [auth A]
AL [auth A],
AM [auth A],
BL [auth A],
BM [auth A],
CL [auth A],
CM [auth A],
DL [auth A],
DM [auth A],
EL [auth A],
EM [auth A],
FL [auth A],
FM [auth A],
GL [auth A],
GM [auth A],
HL [auth A],
HM [auth A],
IL [auth A],
IM [auth A],
JL [auth A],
JM [auth A],
KL [auth A],
KM [auth A],
LL [auth A],
LM [auth A],
ML [auth A],
MM [auth A],
NL [auth A],
NM [auth A],
OL [auth A],
PL [auth A],
QL [auth A],
RL [auth A],
SL [auth A],
TL [auth A],
TM [auth E],
UL [auth A],
VL [auth A],
WK [auth A],
WL [auth A],
WM [auth G],
XK [auth A],
XL [auth A],
YK [auth A],
YL [auth A],
ZK [auth A],
ZL [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [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],
AN [auth L],
BB [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],
CB [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],
CN [auth P],
DA [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],
DN [auth P],
EA [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],
EN [auth P],
FA [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],
FN [auth P],
GA [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 A],
GN [auth Q],
HA [auth A],
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 A],
HN [auth Q],
IA [auth A],
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 A],
IN [auth S],
JA [auth A],
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 A],
JN [auth S],
KA [auth A],
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 A],
KN [auth S],
LA [auth A],
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 A],
LN [auth T],
MA [auth A],
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 A],
MN [auth a],
NA [auth A],
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 A],
NN [auth b],
OA [auth A],
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 A],
OM [auth A],
PA [auth A],
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 A],
PM [auth C],
QA [auth A],
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 A],
RA [auth A],
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],
RK [auth A],
RM [auth D],
SA [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],
SK [auth A],
SM [auth E],
TA [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],
TK [auth A],
UA [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],
UK [auth A],
UM [auth F],
VA [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],
VK [auth A],
VM [auth G],
WA [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],
XA [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],
XM [auth H],
YA [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],
YM [auth H],
ZA [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],
ZM [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0TD
Query on 0TD
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.322α = 90
b = 401.322β = 90
c = 175.648γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM51266
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099687

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Database references
  • Version 1.3: 2016-02-10
    Changes: Database references
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 2.0: 2019-12-25
    Changes: Author supporting evidence, Polymer sequence