4V9B

Crystal Structure of the 70S ribosome with tigecycline.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


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.USA 110: 3812-3816

  • DOI: 10.1073/pnas.1216691110
  • Primary Citation of Related Structures:  4G5K, 4G5L, 4G5M, 4G5N, 4G5T, 4G5U, 4G5V, 4G5W, 4V9A

  • 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 interact ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
AE, CE
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
AF, CF
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
AG, CG
208Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
AH, CH
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
AI, CI
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
AJ, CJ
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
AK, CK
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
AL, CL
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
AM, CM
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
AN, CN
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
AO, CO
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
AP, CP
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
AQ, CQ
61Thermus aquaticusGene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
AR, CR
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
AS, CS
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
AT, CT
105Thermus aquaticusGene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
AU, CU
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
AV, CV
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
AW, CW
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
AX, CX
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD
276Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE, DE
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF, DF
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG, DG
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH, DH
180Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplF
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BK, DK
148Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BM, DM
140Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BN, DN
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BO, DO
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BP, DP
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
B0, D0
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BQ, DQ
112Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BR, DR
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
B1, D1
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
B2, D2
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS, DS
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT, DT
96Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU, DU
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV, DV
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B3, D3
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BZ, DZ
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BW, DW
72Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP6
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BX, DX
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4, D4
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5, D5
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6, D6
54Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7, D7
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8, D8
65Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA,CA1506Thermus thermophilus HB8
Entity ID: 22
MoleculeChainsLengthOrganism
TRNA-FMETAC,AD,CC,CD77Thermus thermophilus HB8
Entity ID: 23
MoleculeChainsLengthOrganism
MRNAA1,C16synthetic construct
Entity ID: 24
MoleculeChainsLengthOrganism
23S ribosomal RNABA,DA2912Thermus thermophilus HB8
Entity ID: 25
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNABB,DB122Thermus thermophilus HB8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
AG, AQ, CG, CQ
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
T1C
Query on T1C

Download SDF File 
Download CCD File 
AA, CA
TIGECYCLINE
C29 H41 N5 O8
FPZLLRFZJZRHSY-HJYUBDRYSA-P
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A1, AA, AC, AD, AG, AH, AN, AQ, AT, B0, B1, B2, B3, B5, B7, B8, BA, BB, BD, BE, BF, BO, BU, CA, CC, CG, CL, CN, CS, CX, D1, D3, D5, D8, DA, DB, DE, DP, DR, DU
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 210.060α = 90.00
b = 450.270β = 90.00
c = 616.890γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXmodel building
PDB_EXTRACTdata extraction
RemDAqdata collection
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2017-11-22
    Type: Refinement description