4V7J image
Deposition Date 2009-11-02
Release Date 2014-07-09
Last Version Date 2024-10-16
Entry Detail
PDB ID:
4V7J
Keywords:
RIBOSOME
Title:
Structure of RelE nuclease bound to the 70S ribosome (precleavage state)
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
(Taxon ID: )Thermus thermophilus HB8 (Taxon ID: 300852)
Thermus thermophilus (Taxon ID: 274)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.30 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
4V7J validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: A0), AD (auth: B0)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60493 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:VA (auth: A1), BD (auth: B1)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60494 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: A2), CD (auth: B2)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:XA (auth: A3), DD (auth: B3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:YA (auth: A4), ED (auth: B4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJE1 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:ZA (auth: A5), FD (auth: B5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80339 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:AB (auth: A6), GD (auth: B6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P35871 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BB (auth: A7), HD (auth: B7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80340 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:CB (auth: A8), ID (auth: B8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SKU1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:DB (auth: A9), JD (auth: B9)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHR2 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:RNA (2848-MER)
Chain IDs:EB (auth: AA), KD (auth: BA)
Chain Length:2848
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:RNA (119-MER)
Chain IDs:FB (auth: AB), LD (auth: BB)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:Z (auth: AC), FC (auth: BC)
Chain Length:229
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP7 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: AD), GC (auth: BD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:BA (auth: AE), HC (auth: BE)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN8 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:CA (auth: AF), IC (auth: BF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN9 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:DA (auth: AG), JC (auth: BG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:EA (auth: AH), KC (auth: BH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY8 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: AI), LC (auth: BI)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:GA (auth: AJ), MC (auth: BJ)
Chain Length:173
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q8VVE3 Pfam ID:PF00466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:HA (auth: AN), NC (auth: BN)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60488 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:IA (auth: AO), OC (auth: BO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP8 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:JA (auth: AP), PC (auth: BP)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:KA (auth: AQ), QC (auth: BQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60489 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:LA (auth: AR), RC (auth: BR)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:MA (auth: AS), SC (auth: BS)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:NA (auth: AT), TC (auth: BT)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60490 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:OA (auth: AU), UC (auth: BU)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60491 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:PA (auth: AV), VC (auth: BV)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P60492 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:QA (auth: AW), WC (auth: BW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP3 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:RA (auth: AX), XC (auth: BX)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:SA (auth: AY), YC (auth: BY)
Chain Length:95
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:TA (auth: AZ), ZC (auth: BZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Polymer Type:polyribonucleotide
Molecule:RNA (1504-MER)
Chain IDs:V (auth: Aa), BC (auth: Ba)
Chain Length:2848
Number of Molecules:2
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:A (auth: Ab), GB (auth: Bb)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80371 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:B (auth: Ac), HB (auth: Bc)
Chain Length:229
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:C (auth: Ad), IB (auth: Bd)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:D (auth: Ae), JB (auth: Be)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:E (auth: Af), KB (auth: Bf)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP8 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:F (auth: Ag), LB (auth: Bg)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P17291 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:G (auth: Ah), MB (auth: Bh)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY9 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:H (auth: Ai), NB (auth: Bi)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80374 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:I (auth: Aj), OB (auth: Bj)
Chain Length:173
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN7 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:J (auth: Ak), PB (auth: Bk)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80376 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:K (auth: Al), QB (auth: Bl)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:L (auth: Am), RB (auth: Bm)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80377 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:M (auth: An), SB (auth: Bn)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY6 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:N (auth: Ao), TB (auth: Bo)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJ76 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:O (auth: Ap), UB (auth: Bp)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJH3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:P (auth: Aq), VB (auth: Bq)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY7 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:Q (auth: Ar), WB (auth: Br)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:R (auth: As), XB (auth: Bs)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:S (auth: At), YB (auth: Bt)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80380 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:T (auth: Au), ZB (auth: Bu)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:RNA (77-MER)
Chain IDs:X (auth: Av), DC (auth: Bv)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:RNA (77-MER)
Chain IDs:Y (auth: Aw), EC (auth: Bw)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*A*AP*AP*AP*AP*UP*GP*(OMU)P*(A2M)P*(OMG)P*AP*AP*AP*A)-3')
Chain IDs:W (auth: Ax), CC (auth: Bx)
Chain Length:96
Number of Molecules:2
Biological Source:
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Toxin relE
Gene (Uniprot):relE
Mutations:R45A, R81A
Chain IDs:U (auth: Ay), AC (auth: By)
Chain Length:95
Number of Molecules:2
Biological Source:Escherichia coli K-12
UniProt ID:P0C077 Pfam ID:PF05016
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MU X U 5-METHYLURIDINE 5'-MONOPHOSPHATE
A2M W A 2'-O-METHYL-ADENOSINE-5'-MONOPHOSPHATE
OMG W G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
OMU W U O2'-METHYLURIDINE 5'-MONOPHOSPHATE
Ligand Molecules
MG
ZN
Primary Citation
The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.
Cell(Cambridge,Mass.) 139 1084 1095 (2009)
PMID: 20005802 DOI: 10.1016/j.cell.2009.11.015

Abstact

Translational control is widely used to adjust gene expression levels. During the stringent response in bacteria, mRNA is degraded on the ribosome by the ribosome-dependent endonuclease, RelE. The molecular basis for recognition of the ribosome and mRNA by RelE and the mechanism of cleavage are unknown. Here, we present crystal structures of E. coli RelE in isolation (2.5 A) and bound to programmed Thermus thermophilus 70S ribosomes before (3.3 A) and after (3.6 A) cleavage. RelE occupies the A site and causes cleavage of mRNA after the second nucleotide of the codon by reorienting and activating the mRNA for 2'-OH-induced hydrolysis. Stacking of A site codon bases with conserved residues in RelE and 16S rRNA explains the requirement for the ribosome in catalysis and the subtle sequence specificity of the reaction. These structures provide detailed insight into the translational regulation on the bacterial ribosome by mRNA cleavage.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4V7J
3KIQ
3KIR
3KIS
3KIT
3KIU
3KIW
3KIX
3KIY