5J4D image
Deposition Date 2016-03-31
Release Date 2016-05-18
Last Version Date 2025-03-19
Entry Detail
PDB ID:
5J4D
Keywords:
RIBOSOME
Title:
E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon
Biological Source:
Source Organism:
Escherichia coli (strain K12) (Taxon ID: 83333)
synthetic construct (Taxon ID: 32630)
Thermus thermophilus HB27 (Taxon ID: 262724)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.10 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 21 21 21
5J4D validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A, EB (auth: FB)
Chain Length:1507
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:AA, EC (auth: FC)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I22 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:AB, ED (auth: FD)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62659 Pfam ID:PF01084
Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:B, FB (auth: GB)
Chain Length:2880
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:BA, FC (auth: GC)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72JR0 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:BB, FD (auth: GD)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62660 Pfam ID:PF00203
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:C, GB (auth: HB)
Chain Length:120
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:CA, GC (auth: HC)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62652 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:CB, GD (auth: HD)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62661 Pfam ID:PF01649
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:D, IA, HB (auth: IB), MC (auth: NC)
Chain Length:77
Number of Molecules:4
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:DA, HC (auth: IC)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72GW3 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:DB, HD (auth: ID)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62613 Pfam ID:PF17070
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:E, IB (auth: JB)
Chain Length:275
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I07 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:EA, IC (auth: JC)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80340 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:F, JB (auth: KB)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I04 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:FA, JC (auth: KC)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72L77 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:G, KB (auth: LB)
Chain Length:205
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I05 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:GA, KC (auth: LC)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I28 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:H, LB (auth: MB)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I16 Pfam ID:PF00281, PF00673
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:HA, LC (auth: MC)
Chain Length:27
Number of Molecules:2
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:I, MB (auth: NB)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I19 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:J, NB (auth: OB)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72GV5 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor 1
Gene (Uniprot):prfA
Chain IDs:JA, NC (auth: OC)
Chain Length:368
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7I0 Pfam ID:PF03462, PF00472
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:K, OB (auth: PB)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72IN1 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:KA, OC (auth: PC)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62662 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:L, PB (auth: QB)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I14 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:LA, PC (auth: QC)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62663 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:M, QB (auth: RB)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I23 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:MA, QC (auth: RC)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62664 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:N, RB (auth: SB)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I11 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:NA, RC (auth: SC)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62665 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:O, SB (auth: TB)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I33 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:OA, SC (auth: TC)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62666 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:P, TB (auth: UB)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I20 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:PA, TC (auth: UC)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62667 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:Q, UB (auth: VB)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72JU9 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:QA, UC (auth: VC)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62668 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:R, VB (auth: WB)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72L76 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:RA, VC (auth: WC)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62669 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:S, WB (auth: XB)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72HR2 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:SA, WC (auth: XC)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62653 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:T, XB (auth: YB)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I09 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:TA, XC (auth: YC)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62654 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:U, YB (auth: ZB)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I06 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:UA, YC (auth: ZC)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P61941 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:V, ZB (auth: AC)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I15 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:VA, ZC (auth: AD)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62655 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:W, AC (auth: BC)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72IA7 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:WA, AD (auth: BD)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62656 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:X, BC (auth: CC)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60493 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:XA, BD (auth: CD)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62657 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:Y, CC (auth: DC)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72G84 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:YA, CD (auth: DD)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62238 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:Z, DC (auth: EC)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:Q72I12 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:ZA, DD (auth: ED)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
UniProt ID:P62658 Pfam ID:PF00366
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD UA ASP modified residue
2MA B A modified residue
2MG A G modified residue
2MU B U modified residue
4OC A C modified residue
4SU D U modified residue
5MC A C modified residue
5MU B U modified residue
7MG A G modified residue
M2G A G modified residue
MA6 A A modified residue
OMG B G modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
MG
ZN
Primary Citation
Structural Basis for Translation Termination on a Pseudouridylated Stop Codon.
J.Mol.Biol. 428 2228 2236 (2016)
PMID: 27107638 DOI: 10.1016/j.jmb.2016.04.018

Abstact

Pseudouridylation of messenger RNA emerges as an abundant modification involved in gene expression regulation. Pseudouridylation of stop codons in eukaryotic and bacterial cells results in stop-codon read through. The structural mechanism of this phenomenon is not known. Here we present a 3.1-Å crystal structure of Escherichia coli release factor 1 (RF1) bound to the 70S ribosome in response to the ΨAA codon. The structure reveals that recognition of a modified stop codon does not differ from that of a canonical stop codon. Our in vitro biochemical results support this finding by yielding nearly identical rates for peptide release from E. coli ribosomes programmed with pseudouridylated and canonical stop codons. The crystal structure also brings insight into E. coli RF1-specific interactions and suggests involvement of L27 in bacterial translation termination. Our results are consistent with a mechanism in which read through of a pseudouridylated stop codon in bacteria results from increased decoding by near-cognate tRNAs (miscoding) rather than from decreased efficiency of termination.

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Protein

Chemical

Disease

Primary Citation of related structures
5J4D