4V9B image
Deposition Date 2012-07-18
Release Date 2014-07-09
Last Version Date 2024-11-06
Entry Detail
PDB ID:
4V9B
Keywords:
RIBOSOME/ANTIBIOTIC
Title:
Crystal Structure of the 70S ribosome with tigecycline.
Biological Source:
Source Organism:
Synthetic construct (Taxon ID: 32630)
Thermus thermophilus (Taxon ID: 300852)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.10 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
4V9B validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:X (auth: A1), ZB (auth: C1)
Chain Length:6
Number of Molecules:2
Biological Source:Synthetic construct
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA), CB (auth: CA)
Chain Length:1506
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:TRNA-FMET
Chain IDs:V (auth: AC), W (auth: AD), XB (auth: CC), YB (auth: CD)
Chain Length:77
Number of Molecules:4
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AE), DB (auth: CE)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AF), EB (auth: CF)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF00189, PF07650
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AG), FB (auth: CG)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AH), GB (auth: CH)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AI), HB (auth: CI)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AJ), IB (auth: CJ)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AK), JB (auth: CK)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AL), KB (auth: CL)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AM), LB (auth: CM)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AN), MB (auth: CN)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AO), NB (auth: CO)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AP), OB (auth: CP)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14
Chain IDs:N (auth: AQ), PB (auth: CQ)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AR), QB (auth: CR)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AS), RB (auth: CS)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AT), SB (auth: CT)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AU), TB (auth: CU)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AV), UB (auth: CV)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AW), VB (auth: CW)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN THX
Gene (Uniprot):rpsU
Chain IDs:U (auth: AX), WB (auth: CX)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:KA (auth: B0), MC (auth: D0)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:NA (auth: B1), PC (auth: D1)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60491 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:OA (auth: B2), QC (auth: D2)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60492 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:TA (auth: B3), VC (auth: D3)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60493 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:XA (auth: B4), ZC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJE1 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:YA (auth: B5), AD (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80339 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:ZA (auth: B6), BD (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P35871 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:AB (auth: B7), CD (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80340 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:BB (auth: B8), DD (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SKU1 Pfam ID:PF01632
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Y (auth: BA), AC (auth: DA)
Chain Length:2912
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:Z (auth: BB), BC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: BD), CC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:BA (auth: BE), DC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN8 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:CA (auth: BF), EC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN9 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:DA (auth: BG), FC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ0 Pfam ID:PF00673, PF00281
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:EA (auth: BH), GC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: BK), HC (auth: DK)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:GA (auth: BM), IC (auth: DM)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60488 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:HA (auth: BN), JC (auth: DN)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP8 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:IA (auth: BO), KC (auth: DO)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:JA (auth: BP), LC (auth: DP)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60489 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:LA (auth: BQ), NC (auth: DQ)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:MA (auth: BR), OC (auth: DR)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60490 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:PA (auth: BS), RC (auth: DS)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP3 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:QA (auth: BT), SC (auth: DT)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:RA (auth: BU), TC (auth: DU)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP9 Pfam ID:PF17136, PF00467
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:SA (auth: BV), UC (auth: DV)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:VA (auth: BW), XC (auth: DW)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:WA (auth: BX), YC (auth: DX)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:UA (auth: BZ), WC (auth: DZ)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60494 Pfam ID:PF00830
Ligand Molecules
MG
T1C
ZN
Primary Citation
Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis.
Proc.Natl.Acad.Sci.USA 110 3812 3816 (2013)
PMID: 23431179 DOI: 10.1073/pnas.1216691110

Abstact

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.

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Disease

Primary Citation of related structures
4V9B
4G5T
4G5U
4G5V
4G5W