4YHH

Crystal structure of the 30S ribosomal subunit from Thermus thermophilus in complex with tigecycline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome.

Schedlbauer, A.Kaminishi, T.Ochoa-Lizarralde, B.Dhimole, N.Zhou, S.Lopez-Alonso, J.P.Connell, S.R.Fucini, P.

(2015) Antimicrob Agents Chemother 59: 2849-2854

  • DOI: 10.1128/AAC.04895-14
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Although both tetracycline and tigecycline inhibit protein synthesis by sterically hindering the binding of tRNA to the ribosomal A site, tigecycline shows increased efficacy in both in vitro and in vivo activity assays and escapes the most common re ...

    Although both tetracycline and tigecycline inhibit protein synthesis by sterically hindering the binding of tRNA to the ribosomal A site, tigecycline shows increased efficacy in both in vitro and in vivo activity assays and escapes the most common resistance mechanisms associated with the tetracycline class of antibiotics. These differences in activities are attributed to the tert-butyl-glycylamido side chain found in tigecycline. Our structural analysis by X-ray crystallography shows that tigecycline binds the bacterial 30S ribosomal subunit with its tail in an extended conformation and makes extensive interactions with the 16S rRNA nucleotide C1054. These interactions restrict the mobility of C1054 and contribute to the antimicrobial activity of tigecycline, including its resistance to the ribosomal protection proteins.


    Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia, Derio, Bizkaia, Spain Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany IKERBASQUE, Basque Foundation for Science, Bilbao, Spain sean.connell@gmail.com pfucini@cicbiogune.es.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
115Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
124Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
N
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
73Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
226Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
V
24Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
E
157Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1507Thermus thermophilus HB8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T1C
Query on T1C

Download CCD File 
A
TIGECYCLINE
C29 H41 N5 O8
FPZLLRFZJZRHSY-HJYUBDRYSA-P
 Ligand Interaction
ZN
Query on ZN

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D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 409.59α = 90
b = 409.59β = 90
c = 171.73γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2016-02-03
    Changes: Database references, Source and taxonomy, Structure summary