RCSB PDB - 4W2F: Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites

 4W2F

Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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Literature

Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome.

Polikanov, Y.S.Osterman, I.A.Szal, T.Tashlitsky, V.N.Serebryakova, M.V.Kusochek, P.Bulkley, D.Malanicheva, I.A.Efimenko, T.A.Efremenkova, O.V.Konevega, A.L.Shaw, K.J.Bogdanov, A.A.Rodnina, M.V.Dontsova, O.A.Mankin, A.S.Steitz, T.A.Sergiev, P.V.

(2014) Mol Cell 56: 531-540

  • DOI: https://doi.org/10.1016/j.molcel.2014.09.020
  • Primary Citation of Related Structures:  
    4W2F, 4W2G, 4W2H

  • PubMed Abstract: 

    We demonstrate that the antibiotic amicoumacin A (AMI) is a potent inhibitor of protein synthesis. Resistance mutations in helix 24 of the 16S rRNA mapped the AMI binding site to the small ribosomal subunit. The crystal structure of bacterial ribosome in complex with AMI solved at 2.4 Å resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16S rRNA in the E site and the mRNA backbone. Simultaneous interactions of AMI with 16S rRNA and mRNA and the in vivo experimental evidence suggest that it may inhibit the progression of the ribosome along mRNA. Consistent with this proposal, binding of AMI interferes with translocation in vitro. The inhibitory action of AMI can be partly compensated by mutations in the translation elongation factor G.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S2B [auth AB],
FB [auth CB]
256Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S3C [auth AC],
GB [auth CC]
239Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S4D [auth AD],
HB [auth CD]
209Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S5E [auth AE],
IB [auth CE]
162Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S6F [auth AF],
JB [auth CF]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S7G [auth AG],
KB [auth CG]
156Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S8H [auth AH],
LB [auth CH]
138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S9I [auth AI],
MB [auth CI]
128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S10J [auth AJ],
NB [auth CJ]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S11K [auth AK],
OB [auth CK]
129Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S12L [auth AL],
PB [auth CL]
132Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S13M [auth AM],
QB [auth CM]
126Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S14N [auth AN],
RB [auth CN]
61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S15O [auth AO],
SB [auth CO]
89Thermus 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
30S Ribosomal Protein S16P [auth AP],
TB [auth CP]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S17Q [auth AQ],
UB [auth CQ]
105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S18R [auth AR],
VB [auth CR]
88Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S19S [auth AS],
WB [auth CS]
93Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein S20T [auth AT],
XB [auth CT]
106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S Ribosomal Protein THXU [auth AU],
YB [auth CU]
27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L2BA [auth BD],
FC [auth DD]
276Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L3CA [auth BE],
GC [auth DE]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L4DA [auth BF],
HC [auth DF]
210Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L5EA [auth BG],
IC [auth DG]
182Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L6FA [auth BH],
JC [auth DH]
180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L9GA [auth BI],
KC [auth DI]
148Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L13HA [auth BN],
LC [auth DN]
140Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L14IA [auth BO],
MC [auth DO]
122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L15JA [auth BP],
NC [auth DP]
150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L16KA [auth BQ],
OC [auth DQ]
141Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L17LA [auth BR],
PC [auth DR]
118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L18MA [auth BS],
QC [auth DS]
112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L19NA [auth BT],
RC [auth DT]
146Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L20OA [auth BU],
SC [auth DU]
118Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L21PA [auth BV],
TC [auth DV]
101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L22QA [auth BW],
UC [auth DW]
113Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L23RA [auth BX],
VC [auth DX]
96Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L24SA [auth BY],
WC [auth DY]
110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L25TA [auth BZ],
XC [auth DZ]
206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L27UA [auth B0],
YC [auth D0]
85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L28VA [auth B1],
ZC [auth D1]
98Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L29AD [auth D2],
WA [auth B2]
72Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L30BD [auth D3],
XA [auth B3]
60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L31CD [auth D4],
YA [auth B4]
71Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L32DD [auth D5],
ZA [auth B5]
60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L33AB [auth B6],
ED [auth D6]
54Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L34BB [auth B7],
FD [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L35CB [auth B8],
GD [auth D8]
65Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L36DB [auth B9],
HD [auth D9]
37Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UAM
Query on UAM

Download Ideal Coordinates CCD File 
FM [auth AA],
WKB [auth CA]
Amicoumacin A
C20 H29 N3 O7
DCPWYLSPIAHJFU-YKRRISCLSA-N
SF4
Query on SF4

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KM [auth AD],
XKB [auth CD]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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BDB [auth B9]
FOC [auth DY]
JLB [auth CN]
LCB [auth B4]
LOC [auth D4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
BN [auth AX],
ULB [auth CX]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AAA [auth BA]
AAB [auth BP]
AAC [auth DA]
ABA [auth BA]
ABB [auth BU]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.06α = 90
b = 448.57β = 90
c = 623.95γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UAMClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2015-01-14
    Changes: Database references
  • Version 2.0: 2019-07-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations