6OXA image
Deposition Date 2019-05-13
Release Date 2019-08-21
Last Version Date 2024-10-30
Entry Detail
PDB ID:
6OXA
Keywords:
Title:
Dimeric E.coli YoeB bound to Thermus thermophilus 70S pre-cleavage (AAU)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.25 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: QA), AB (auth: XA)
Chain Length:1521
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: QB), BB (auth: XB)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: QC), CB (auth: XC)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: QD), DB (auth: XD)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: QE), EB (auth: XE)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: QF), FB (auth: XF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: QG), GB (auth: XG)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: QH), HB (auth: XH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: QI), IB (auth: XI)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: QJ), JB (auth: XJ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: QK), KB (auth: XK)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:L (auth: QM), MB (auth: XM)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:M (auth: QN), NB (auth: XN)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:N (auth: QO), OB (auth: XO)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:O (auth: QP), PB (auth: XP)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:P (auth: QQ), QB (auth: XQ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:Q (auth: QR), RB (auth: XR)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:R (auth: QS), DD (auth: XS)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:S (auth: QT), SB (auth: XT)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:T (auth: QU), TB (auth: XU)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:P-site tRNA-fMet
Chain IDs:U (auth: QV), V (auth: QW), UB (auth: XV), VB (auth: XW)
Chain Length:77
Number of Molecules:4
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:W (auth: QX), WB (auth: XX)
Chain Length:22
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Addiction module toxin, Txe/YoeB family
Gene (Uniprot):yoeB
Chain IDs:X (auth: QY), Y (auth: QZ), XB (auth: XY), YB (auth: XZ)
Chain Length:84
Number of Molecules:4
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: R0), ZB (auth: Y0)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:AA (auth: R2), BC (auth: Y2)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:BA (auth: R3), CC (auth: Y3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:CA (auth: R4), DC (auth: Y4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:DA (auth: R5), EC (auth: Y5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:EA (auth: R6), FC (auth: Y6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:FA (auth: R7), GC (auth: Y7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:GA (auth: R9), IC (auth: Y9)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:HA (auth: RA), JC (auth: YA)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:IA (auth: RB), KC (auth: YB)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:JA (auth: RD), YC (auth: YD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:KA (auth: RE), CD (auth: YE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:LA (auth: RG), MC (auth: YG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:MA (auth: RH), AD (auth: YH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:NA (auth: RI), NC (auth: YI)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:OA (auth: RN), OC (auth: YN)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:PA (auth: RO), PC (auth: YO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:QA (auth: RP), XC (auth: YP)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:RA (auth: RQ), ZC (auth: YQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:SA (auth: RR), QC (auth: YR)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:TA (auth: RS), RC (auth: YS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:UA (auth: RT), SC (auth: YT)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:VA (auth: RU), TC (auth: YU)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:WA (auth: RV), BD (auth: YV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:XA (auth: RW), UC (auth: YW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:YA (auth: RX), VC (auth: YX)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:ZA (auth: RY), WC (auth: YY)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:GD (auth: RZ), HD (auth: YZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:LB (auth: XL), ID (auth: QL)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:AC (auth: Y1), ED (auth: R1)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:HC (auth: Y8), LD (auth: R8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:LC (auth: YF), FD (auth: RF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:CCPuro
Chain IDs:JD (auth: ZA), KD (auth: ZB)
Chain Length:3
Number of Molecules:2
Biological Source:Streptomyces alboniger
Primary Citation
Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
Nucleic Acids Res. 47 10400 10413 (2019)
PMID: 31501867 DOI: 10.1093/nar/gkz760

Abstact

Chromosomally-encoded toxin-antitoxin complexes are ubiquitous in bacteria and regulate growth through the release of the toxin component typically in a stress-dependent manner. Type II ribosome-dependent toxins adopt a RelE-family RNase fold and inhibit translation by degrading mRNAs while bound to the ribosome. Here, we present biochemical and structural studies of the Escherichia coli YoeB toxin interacting with both a UAA stop and an AAU sense codon in pre- and post-mRNA cleavage states to provide insights into possible mRNA substrate selection. Both mRNAs undergo minimal changes during the cleavage event in contrast to type II ribosome-dependent RelE toxin. Further, the 16S rRNA decoding site nucleotides that monitor the mRNA in the aminoacyl(A) site adopt different orientations depending upon which toxin is present. Although YoeB is a RelE family member, it is the sole ribosome-dependent toxin that is dimeric. We show that engineered monomeric YoeB is active against mRNAs bound to both the small and large subunit. However, the stability of monomeric YoeB is reduced ∼20°C, consistent with potential YoeB activation during heat shock in E. coli as previously demonstrated. These data provide a molecular basis for the ability of YoeB to function in response to thermal stress.

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Disease

Primary Citation of related structures