4JI8

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

The central role of protein S12 in organizing the structure of the decoding site of the ribosome.

Demirci, H., Wang, L., Murphy, F.V., Murphy, E.L., Carr, J.F., Blanchard, S.C., Jogl, G., Dahlberg, A.E., Gregory, S.T.

(2013) RNA 19: 1791-1801

  • DOI: https://doi.org/10.1261/rna.040030.113
  • Primary Citation of Related Structures:  
    4JI0, 4JI1, 4JI2, 4JI3, 4JI4, 4JI5, 4JI6, 4JI7, 4JI8

  • PubMed Abstract: 

    The ribosome decodes mRNA by monitoring the geometry of codon-anticodon base-pairing using a set of universally conserved 16S rRNA nucleotides within the conformationally dynamic decoding site. By applying single-molecule FRET and X-ray crystallography, we have determined that conditional-lethal, streptomycin-dependence mutations in ribosomal protein S12 interfere with tRNA selection by allowing conformational distortions of the decoding site that impair GTPase activation of EF-Tu during the tRNA selection process. Distortions in the decoding site are reversed by streptomycin or by a second-site suppressor mutation in 16S rRNA. These observations encourage a refinement of the current model for decoding, wherein ribosomal protein S12 and the decoding site collaborate to optimize codon recognition and substrate discrimination during the early stages of the tRNA selection process.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S2256Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S3239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S4209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S5162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S6101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S7156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S8138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S9128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S10105Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S11129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S12135Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S13126Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1461Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1589Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1688Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S17105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1888Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S1993Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S20106Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN THX27Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,522Thermus thermophilus HB8
Sequence Annotations
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SRY
Query on SRY
Download Ideal Coordinates CCD File 
V [auth A]STREPTOMYCIN
C21 H39 N7 O12
UCSJYZPVAKXKNQ-HZYVHMACSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CP [auth D],
PP [auth N]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AA [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],
AL [auth A],
AM [auth A],
AN [auth A],
AO [auth A],
AP [auth C],
BA [auth A],
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],
BL [auth A],
BM [auth A],
BN [auth A],
BO [auth A],
BP [auth C],
CA [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],
CL [auth A],
CM [auth A],
CN [auth A],
CO [auth A],
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],
DL [auth A],
DM [auth A],
DN [auth A],
DO [auth A],
DP [auth D],
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],
EL [auth A],
EM [auth A],
EN [auth A],
EO [auth A],
EP [auth D],
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],
FL [auth A],
FM [auth A],
FN [auth A],
FO [auth A],
FP [auth D],
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],
GL [auth A],
GM [auth A],
GN [auth A],
GO [auth A],
GP [auth D],
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],
HL [auth A],
HM [auth A],
HN [auth A],
HO [auth A],
HP [auth D],
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],
IL [auth A],
IM [auth A],
IN [auth A],
IO [auth A],
IP [auth D],
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],
JL [auth A],
JM [auth A],
JN [auth A],
JO [auth A],
JP [auth E],
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],
KL [auth A],
KM [auth A],
KN [auth A],
KO [auth A],
KP [auth E],
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],
LL [auth A],
LM [auth A],
LN [auth A],
LO [auth A],
LP [auth E],
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],
ML [auth A],
MM [auth A],
MN [auth A],
MO [auth A],
MP [auth F],
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],
NL [auth A],
NM [auth A],
NN [auth A],
NO [auth A],
NP [auth H],
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],
OL [auth A],
OM [auth A],
ON [auth A],
OO [auth A],
OP [auth L],
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],
PL [auth A],
PM [auth A],
PN [auth A],
PO [auth A],
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],
QL [auth A],
QM [auth A],
QN [auth A],
QO [auth A],
QP [auth N],
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],
RL [auth A],
RM [auth A],
RN [auth A],
RO [auth A],
RP [auth O],
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],
SL [auth A],
SM [auth A],
SN [auth A],
SO [auth A],
SP [auth P],
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],
TL [auth A],
TM [auth A],
TN [auth A],
TO [auth A],
TP [auth Q],
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],
UL [auth A],
UM [auth A],
UN [auth A],
UO [auth A],
UP [auth Q],
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],
VL [auth A],
VM [auth A],
VN [auth A],
VO [auth B],
VP [auth S],
W [auth A],
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],
WK [auth A],
WL [auth A],
WM [auth A],
WN [auth A],
WO [auth B],
X [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],
XK [auth A],
XL [auth A],
XM [auth A],
XN [auth A],
XO [auth B],
Y [auth A],
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],
YK [auth A],
YL [auth A],
YM [auth A],
YN [auth A],
YO [auth C],
Z [auth A],
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],
ZK [auth A],
ZL [auth A],
ZM [auth A],
ZN [auth A],
ZO [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.74 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 400.305α = 90
b = 400.305β = 90
c = 214.785γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations