ISDA: 4YPB

Deposition Date 2015-03-12

Release Date 2015-10-21

Last Version Date 2023-09-27

Entry Detail

PDB ID:

4YPB

Keywords:

RIBOSOME

Title:

Precleavage 70S structure of the P. vulgaris HigB DeltaH92 toxin bound to the AAA codon

Biological Source:

Source Organism(s):

Proteus vulgaris (Taxon ID: 585)
Escherichia coli (Taxon ID: 562)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.40 Å

R-Value Free:

0.23

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: QA), EB (auth: XA)
Chain Length:1522
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: QB), FB (auth: XB)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QC), GB (auth: XC)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: QD), HB (auth: XD)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QE), IB (auth: XE)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QF), JB (auth: XF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QG), KB (auth: XG)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P17291 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:H (auth: QH), LB (auth: XH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: QI), MB (auth: XI)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QJ), NB (auth: XJ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QK), OB (auth: XK)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QL), PB (auth: XL)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QM), QB (auth: XM)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80377 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:N (auth: QN), RB (auth: XN)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: QO), SB (auth: XO)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QP), TB (auth: XP)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:Q (auth: QQ), UB (auth: XQ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: QR), VB (auth: XR)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QS), WB (auth: XS)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QT), XB (auth: XT)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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: QU), YB (auth: XU)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:tRNA fMet
Chain IDs:V (auth: QV), W (auth: QW), ZB (auth: XV), AC (auth: XW)
Chain Length:77
Number of Molecules:4
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:messenger RNA
Chain IDs:X (auth: QX), BC (auth: XX)
Chain Length:25
Number of Molecules:2
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Host inhibition of growth B
Gene (Uniprot):higB
Mutagens:delta H92
Chain IDs:Y (auth: QY), CC (auth: XY)
Chain Length:117
Number of Molecules:2
Biological Source:Proteus vulgaris

UniProt ID:Q7A225 Pfam ID:PF05015

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: R0), YC (auth: Y0)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60493 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:VA (auth: R1), ZC (auth: Y1)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60494 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: R2), AD (auth: Y2)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:XA (auth: R3), BD (auth: Y3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:YA (auth: R4), CD (auth: Y4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:ZA (auth: R5), DD (auth: Y5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:AB (auth: R6), ED (auth: Y6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:BB (auth: R7), FD (auth: Y7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:CB (auth: R8), GD (auth: Y8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SKU1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:DB (auth: R9), HD (auth: Y9)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHR2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:Z (auth: RA), DC (auth: YA)
Chain Length:2916
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:AA (auth: RB), EC (auth: YB)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:BA (auth: RD), FC (auth: YD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:CA (auth: RE), GC (auth: YE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:DA (auth: RF), HC (auth: YF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:EA (auth: RG), IC (auth: YG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:FA (auth: RH), JC (auth: YH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:GA (auth: RI), KC (auth: YI)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SLQ1 Pfam ID:PF03948, PF01281

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:HA (auth: RN), LC (auth: YN)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:IA (auth: RO), MC (auth: YO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:JA (auth: RP), NC (auth: YP)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:KA (auth: RQ), OC (auth: YQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60489 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:LA (auth: RR), PC (auth: YR)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:MA (auth: RS), QC (auth: YS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:NA (auth: RT), RC (auth: YT)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60490 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:OA (auth: RU), SC (auth: YU)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:PA (auth: RV), TC (auth: YV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60492 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:QA (auth: RW), UC (auth: YW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:RA (auth: RX), VC (auth: YX)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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:SA (auth: RY), WC (auth: YY)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:TA (auth: RZ), XC (auth: YZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Ligand Molecules

Primary Citation

Defining the mRNA recognition signature of a bacterial toxin protein.

Schureck, M.A, Dunkle, J.A, Maehigashi, T, Miles, S.J, Dunham, C.M.Show

Proc.Natl.Acad.Sci.USA 112 13862 13867 (2015)

PMID: 26508639 DOI: 10.1073/pnas.1512959112

Abstact

Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. Here, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop to recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

Feedback Form