1N32

Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form

Ogle, J.M.Murphy IV, F.V.Tarry, M.J.Ramakrishnan, V.

(2002) Cell 111: 721-732

  • DOI: 10.1016/s0092-8674(02)01086-3
  • Primary Citation of Related Structures:  
    1N32, 1N33, 1N34, 1N36

  • PubMed Abstract: 
  • A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution ...

    A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.


    Related Citations: 
    • Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
      Ogle, J.M., Brodersen, D.E., Clemons Jr., W.M., Tarry, M.J., Carter, A.P., Ramakrishnan, V.
      (2001) Science 292: 897
    • Structure of the 30S Ribosomal Subunit
      Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R., Carter, A.P., Vonrhein, C., Hartsch, T., Ramakrishnan, V.
      (2000) Nature 407: 327
    • Functional Insights from the Structure of the 30S Ribosomal Subunit and its Interactions with Antibiotics
      Carter, A.P., Clemons Jr., W.M., Brodersen, D.E., Wimberly, B.T., Morgan-Warren, R., Ramakrishnan, V.
      (2000) Nature 407: 340

    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2D [auth B]256Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80371 
Go to UniProtKB:  P80371
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80371
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3E [auth C]239Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80372 
Go to UniProtKB:  P80372
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80372
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4F [auth D]208Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80373 
Go to UniProtKB:  P80373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80373
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5G [auth E]161Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHQ5 
Go to UniProtKB:  Q5SHQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHQ5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6H [auth F]101Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLP8 
Go to UniProtKB:  Q5SLP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLP8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7I [auth G]155Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P17291 
Go to UniProtKB:  P17291
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17291
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8J [auth H]138Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P0DOY9 
Go to UniProtKB:  P0DOY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9K [auth I]128Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80374 
Go to UniProtKB:  P80374
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80374
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10L [auth J]104Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN7 
Go to UniProtKB:  Q5SHN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHN7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11M [auth K]129Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80376 
Go to UniProtKB:  P80376
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80376
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12N [auth L]135Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN3 
Go to UniProtKB:  Q5SHN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHN3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13O [auth M]126Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80377 
Go to UniProtKB:  P80377
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80377
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14P [auth N]60Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P0DOY6 
Go to UniProtKB:  P0DOY6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15Q [auth O]88Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJ76 
Go to UniProtKB:  Q5SJ76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJ76
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16R [auth P]88Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJH3 
Go to UniProtKB:  Q5SJH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SJH3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17S [auth Q]104Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P0DOY7 
Go to UniProtKB:  P0DOY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOY7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18T [auth R]88Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLQ0 
Go to UniProtKB:  Q5SLQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLQ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19U [auth S]92Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHP2 
Go to UniProtKB:  Q5SHP2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHP2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20V [auth T]106Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P80380 
Go to UniProtKB:  P80380
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80380
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXW [auth V]26Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIH3 
Go to UniProtKB:  Q5SIH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIH3
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA 1522Thermus thermophilus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
ANTICODON STEM-LOOP OF LEU-2 TRANSFER RNAB [auth Y]17Thermus thermophilus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
A-SITE MESSENGER RNA FRAGMENTC [auth Z]6Thermus thermophilus
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
X [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BG [auth N],
XF [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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 M],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth Y],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth D],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth E],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RNA PDBBind:  1N32 Kd: 1.90e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 400.296α = 90
b = 400.296β = 90
c = 175.483γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Database references, Derived calculations