4V9A

Crystal Structure of the 70S ribosome with tetracycline.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis.

Jenner, L.Starosta, A.L.Terry, D.S.Mikolajka, A.Filonava, L.Yusupov, M.Blanchard, S.C.Wilson, D.N.Yusupova, G.

(2013) Proc Natl Acad Sci U S A 110: 3812-3816

  • DOI: 10.1073/pnas.1216691110
  • Primary Citation of Related Structures:  
    4V9A, 4V9B

  • PubMed Abstract: 
  • Here we present an X-ray crystallography structure of the clinically relevant tigecycline antibiotic bound to the 70S ribosome. Our structural and biochemical analysis indicate that the enhanced potency of tigecycline results from a stacking interaction with nucleobase C1054 within the decoding site of the ribosome ...

    Here we present an X-ray crystallography structure of the clinically relevant tigecycline antibiotic bound to the 70S ribosome. Our structural and biochemical analysis indicate that the enhanced potency of tigecycline results from a stacking interaction with nucleobase C1054 within the decoding site of the ribosome. Single-molecule fluorescence resonance energy transfer studies reveal that, during decoding, tigecycline inhibits the initial codon recognition step of tRNA accommodation and prevents rescue by the tetracycline-resistance protein TetM.


    Organizational Affiliation

    Institut National de la Santé et de la Recherche Médicale U964, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7104, 67404 Illkirch, France.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B [auth AE],
CB [auth CE]
256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C [auth AF],
DB [auth CF]
239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D [auth AG],
EB [auth CG]
208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E [auth AH],
FB [auth CH]
162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F [auth AI],
GB [auth CI]
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G [auth AJ],
HB [auth CJ]
156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H [auth AK],
IB [auth CK]
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I [auth AL],
JB [auth CL]
128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J [auth AM],
KB [auth CM]
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K [auth AN],
LB [auth CN]
129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L [auth AO],
MB [auth CO]
128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M [auth AP],
NB [auth CP]
126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14N [auth AQ],
OB [auth CQ]
61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O [auth AR],
PB [auth CR]
89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P [auth AS],
QB [auth CS]
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q [auth AT],
RB [auth CT]
105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R [auth AU],
SB [auth CU]
88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S [auth AV],
TB [auth CV]
93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20T [auth AW],
UB [auth CW]
106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXU [auth AX],
VB [auth CX]
27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2Z [auth BD],
AC [auth DD]
276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3AA [auth BE],
BC [auth DE]
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4BA [auth BF],
CC [auth DF]
210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5CA [auth BG],
DC [auth DG]
182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6DA [auth BH],
EC [auth DH]
180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9EA [auth BK],
FC [auth DK]
148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13FA [auth BM],
GC [auth DM]
140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14GA [auth BN],
HC [auth DN]
122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15HA [auth BO],
IC [auth DO]
150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16IA [auth BP],
JC [auth DP]
141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
UniProt
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17JA [auth B0],
KC [auth D0]
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18KA [auth BQ],
LC [auth DQ]
112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
UniProt
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19LA [auth BR],
MC [auth DR]
146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20MA [auth B1],
NC [auth D1]
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
UniProt
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21NA [auth B2],
OC [auth D2]
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22OA [auth BS],
PC [auth DS]
113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PA [auth BT],
QC [auth DT]
96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24QA [auth BU],
RC [auth DU]
110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25RA [auth BV],
SC [auth DV]
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27SA [auth B3],
TC [auth D3]
85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28TA [auth BZ],
UC [auth DZ]
98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29UA [auth BW],
VC [auth DW]
72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30VA [auth BX],
WC [auth DX]
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31WA [auth B4],
XC [auth D4]
71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32XA [auth B5],
YC [auth D5]
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33YA [auth B6],
ZC [auth D6]
54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34ZA [auth B7],
AD [auth D7]
49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
UniProt
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35AB [auth B8],
BD [auth D8]
65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth AA],
BB [auth CA]
1,506Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
TRNA-FMETV [auth AC],
WB [auth CC]
77Thermus thermophilus HB8
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Entity ID: 23
MoleculeChainsLengthOrganismImage
MRNAW [auth A1],
XB [auth C1]
4synthetic construct
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Entity ID: 24
MoleculeChainsLengthOrganismImage
23S ribosomal RNAX [auth BA],
YB [auth DA]
2,912Thermus thermophilus HB8
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Entity ID: 25
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAY [auth BB],
ZB [auth DB]
122Thermus thermophilus HB8
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAC
Query on TAC

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AM [auth AA],
MUA [auth CA]
TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N
 Ligand Interaction
ZN
Query on ZN

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DM [auth AG],
JM [auth AQ],
PUA [auth CG],
RUA [auth CQ]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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