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 

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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

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2D [auth B]256Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3E [auth C]239Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4F [auth D]208Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5G [auth E]161Thermus thermophilusMutation(s): 0 
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Entity ID: 8
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30S RIBOSOMAL PROTEIN S6H [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 9
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30S RIBOSOMAL PROTEIN S7I [auth G]155Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8J [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S9K [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S10L [auth J]104Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11M [auth K]129Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12N [auth L]135Thermus thermophilusMutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S13O [auth M]126Thermus thermophilusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14P [auth N]60Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15Q [auth O]88Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16R [auth P]88Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17S [auth Q]104Thermus thermophilusMutation(s): 0 
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S18T [auth R]88Thermus thermophilusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19U [auth S]92Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 22
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30S RIBOSOMAL PROTEIN S20V [auth T]106Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXW [auth V]26Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1522Thermus thermophilus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
ANTICODON STEM-LOOP OF LEU-2 TRANSFER RNAB [auth Y]17Thermus thermophilus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
A-SITE MESSENGER RNA FRAGMENTC [auth Z]6Thermus thermophilus
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR (Subject of Investigation/LOI)
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] , AF [auth A] , AG [auth M] , BA [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

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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