4V5K image
Deposition Date 2010-05-29
Release Date 2014-07-09
Last Version Date 2024-11-13
Entry Detail
PDB ID:
4V5K
Keywords:
RIBOSOME
Title:
Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
Escherichia coli (Taxon ID: 562)
synthetic construct (Taxon ID: 32630)
Thermus thermophilus HB8 (Taxon ID: 300852)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.20 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
4V5K validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA), GB (auth: CA)
Chain Length:1522
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), HB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AC), IB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AD), JB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AE), KB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AF), LB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AG), MB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P17291 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AH), NB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), OB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AJ), PB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AK), QB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AL), RB (auth: CL)
Chain Length:135
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AM), SB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14 TYPE Z
Chain IDs:N (auth: AN), TB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), UB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AP), VB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJH3 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AQ), WB (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), XB (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AS), YB (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AT), ZB (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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: AU), AC (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:E-SITE TRNA PHE OR P-SITE TRNA PHE
Chain IDs:V (auth: AV), W (auth: AW), BC (auth: CV), CC (auth: CW)
Chain Length:77
Number of Molecules:4
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:X (auth: AX)
Chain Length:25
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:COLICIN-E3
Gene (Uniprot):ceaC
Mutagens:YES
Chain IDs:Y (auth: AY), EC (auth: CY)
Chain Length:97
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P00646 Pfam ID:PF09000
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: B0), FC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:AA (auth: B1), GC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:BA (auth: B2), HC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:CA (auth: B3), IC (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:DA (auth: B4), JC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:EA (auth: B5), KC (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:FA (auth: B6), LC (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:GA (auth: B7), MC (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:HA (auth: B8), NC (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:IA (auth: B9), OC (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHR2 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:JA (auth: BA), PC (auth: DA)
Chain Length:2848
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:KA (auth: BB), QC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L1
Gene (Uniprot):rplA
Chain IDs:LA (auth: BC), RC (auth: DC)
Chain Length:229
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP7 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L2
Gene (Uniprot):rplB
Chain IDs:MA (auth: BD), SC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:NA (auth: BE), TC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:OA (auth: BF), UC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:PA (auth: BG), VC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L6
Chain IDs:QA (auth: BH), WC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L9
Gene (Uniprot):rplI
Chain IDs:RA (auth: BI), XC (auth: DI)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L10
Chain IDs:SA (auth: BJ), YC (auth: DJ)
Chain Length:131
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L13
Gene (Uniprot):rplM
Chain IDs:TA (auth: BN), ZC (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:UA (auth: BO), AD (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:VA (auth: BP), BD (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:WA (auth: BQ), CD (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:XA (auth: BR), DD (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:YA (auth: BS), ED (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:ZA (auth: BT), FD (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:AB (auth: BU), GD (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:BB (auth: BV), HD (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:CB (auth: BW), ID (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:DB (auth: BX), JD (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:EB (auth: BY), KD (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
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:FB (auth: BZ), LD (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:DC (auth: CX)
Chain Length:25
Number of Molecules:1
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A3P A A ADENOSINE-3'-5'-DIPHOSPHATE
Ligand Molecules
MG
ZN
Primary Citation
Structural Basis for 16S Ribosomal RNA Cleavage by the Cytotoxic Domain of Colicin E3.
Nat.Struct.Mol.Biol. 17 1241 1246 (2010)
PMID: 20852642 DOI: 10.1038/nsmb.1896

Abstact

The toxin colicin E3 targets the 30S subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. We present the crystal structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase). The structure reveals how the rRNase domain of colicin binds to the A site of the decoding center in the 70S ribosome and cleaves the 16S ribosomal RNA (rRNA) between A1493 and G1494. The cleavage mechanism involves the concerted action of conserved residues Glu62 and His58 of the cytotoxic domain of colicin E3. These residues activate the 16S rRNA for 2' OH-induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4V5K
2XFZ
2XG0
2XG1
2XG2
1IBK
1IBL
1JCH
2UUC
2WDK
2J02
1J5E
2WRQ
2J00
1HNX
2B9O
2X9T
2WH3
2UUB
1VOV
1EMI
1PNX
2V46
2VQF
2WH1
1N32
2WRN
2F4V
2JL5
1TWT
1E44
1QZC
2UXD
1FKA
1FJG
2UXC
1N36
1HNW
1L1U
1HR0
2V48
2B64
1XMQ
2B9M
1PN8
2WDG
1XNR
1HNZ
1DV4
1RSS
2WDH
1JGQ
1I94
1I96
2UU9
1PN7
1EG0
1IBM
1UJW
2UXB
2VQE
1G1X
2UUA
1I95
1XNQ
1QD7
1GIX
1JGO
1JGP
2X9R
1N34
1N33
1PNS
2JL7
1YL4
2WDM
1XMO
1I97