4W2I

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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This is version 2.1 of the entry. See complete history


Literature

Negamycin Interferes with Decoding and Translocation by Simultaneous Interaction with rRNA and tRNA.

Polikanov, Y.S.Szal, T.Jiang, F.Gupta, P.Matsuda, R.Shiozuka, M.Steitz, T.A.Vazquez-Laslop, N.Mankin, A.S.

(2014) Mol Cell 56: 541-550

  • DOI: https://doi.org/10.1016/j.molcel.2014.09.021
  • Primary Citation of Related Structures:  
    4W2I

  • PubMed Abstract: 

    Negamycin (NEG) is a ribosome-targeting antibiotic that exhibits clinically promising activity. Its binding site and mode of action have remained unknown. We solved the structure of the Thermus thermophilus ribosome bound to mRNA and three tRNAs, in complex with NEG. The drug binds to both small and large ribosomal subunits at nine independent sites. Resistance mutations in the 16S rRNA unequivocally identified the binding site in the vicinity of the conserved helix 34 (h34) in the small subunit as the primary site of antibiotic action in the bacterial and, possibly, eukaryotic ribosome. At this site, NEG contacts 16S rRNA as well as the anticodon loop of the A-site tRNA. Although the NEG site of action overlaps with that of tetracycline (TET), the two antibiotics exhibit different activities: while TET sterically hinders binding of aminoacyl-tRNA to the ribosome, NEG stabilizes its binding, thereby inhibiting translocation and stimulating miscoding.


  • 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
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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
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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 
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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 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L22QA [auth BW],
UC [auth DW]
113Thermus thermophilus HB8Mutation(s): 0 
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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 
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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
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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
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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
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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
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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
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L34BB [auth B7],
FD [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
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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
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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
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S Ribosomal RNAA [auth AA],
EB [auth CA]
1,521Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
mRNAV [auth AV],
ZB [auth CV]
24synthetic construct
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Entity ID: 23
MoleculeChains LengthOrganismImage
A/P-site tRNAAC [auth CW],
CC [auth CY],
W [auth AW],
Y [auth AY]
76Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
E-site tRNABC [auth CX],
X [auth AX]
77Escherichia coli
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S Ribosomal RNADC [auth DA],
Z [auth BA]
2,915Thermus thermophilus HB8
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S Ribosomal RNAAA [auth BB],
EC [auth DB]
121Thermus thermophilus HB8
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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BDB [auth CD],
ZL [auth AD]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
NEG
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EN [auth AX]
LDB [auth CW]
PCB [auth CA]
PL [auth AA]
QCB [auth CA]
EN [auth AX],
LDB [auth CW],
PCB [auth CA],
PL [auth AA],
QCB [auth CA],
QDB [auth CX],
QL [auth AA],
QM [auth AW],
RCB [auth CA],
RL [auth AA],
SCB [auth CA],
SL [auth AA],
TCB [auth CA],
TL [auth AA],
UCB [auth CA],
UL [auth AA],
VCB [auth CA],
VL [auth AA],
WCB [auth CA]
NEGAMYCIN
C9 H20 N4 O4
IKHFJPZQZVMLRH-RNFRBKRXSA-N
ZN
Query on ZN

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AWA [auth B9]
BEC [auth D9]
BVA [auth BY]
FM [auth AN]
HDB [auth CN]
AWA [auth B9],
BEC [auth D9],
BVA [auth BY],
FM [auth AN],
HDB [auth CN],
LVA [auth B4],
RDC [auth DY],
RVA [auth B5],
UVA [auth B6],
VDC [auth D4],
WDC [auth D5],
YDC [auth D6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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NDB [auth CX],
SM [auth AX]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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