ISDA: 5NP6

Deposition Date 2017-04-13

Release Date 2017-06-14

Last Version Date 2025-03-19

Entry Detail

PDB ID:

5NP6

Keywords:

RIBOSOME

Title:

70S structure prior to bypassing

Biological Source:

Source Organism(s):

Escherichia coli (Taxon ID: 83333)
Enterobacteria phage T4 (Taxon ID: 10665)
Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:AB (auth: 0)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:BB (auth: 1)
Chain Length:64
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:CB (auth: 2)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7Q6 Pfam ID:PF00444

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:DB (auth: 3)
Chain Length:131
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7J3 Pfam ID:PF00466

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:EB (auth: 4)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M9 Pfam ID:PF01197

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:A
Chain Length:271
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:P-site tRNA-Gly
Chain IDs:B
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA topoisomerase small subunit
Gene (Uniprot):60
Chain IDs:C
Chain Length:46
Number of Molecules:1
Biological Source:Enterobacteria phage T4

UniProt ID:P23992

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:D
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:E
Chain Length:218
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V0 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:F
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V3 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:G
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V8 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:H
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W1 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:I
Chain Length:122
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:J
Chain Length:151
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:L
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:M
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:N
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:O
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:P
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:Q
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:R
Chain Length:93
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ4 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:S
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:T
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:U
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:V
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:W
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:X
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P68679 Pfam ID:PF01165

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Y
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:Z
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: a)
Chain Length:271
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60422 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:BA (auth: b)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:CA (auth: c)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:DA (auth: d)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:EA (auth: e)
Chain Length:218
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: f)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:GA (auth: g)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:HA (auth: h)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AA10 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: i)
Chain Length:122
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADY3 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: j)
Chain Length:151
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02413 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: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADY7 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: l)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG44 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: m)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0C018 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: n)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7K6 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: o)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L3 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: p)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG48 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: q)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P61175 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: r)
Chain Length:93
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ0 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: s)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60624 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: t)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: u)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L8 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: v)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M2 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: w)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M6 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: x)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG51 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:YA (auth: y)
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N4 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:ZA (auth: z)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N9 Pfam ID:PF00471

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
1MG	Y	G	modified residue
2MA	Y	A	modified residue
2MG	D	G	modified residue
3TD	Y	U	modified residue
4OC	D	C	modified residue
5MC	D	C	modified residue
5MU	Y	U	modified residue
6MZ	Y	A	modified residue
7MG	D	G	modified residue
H2U	Y	U	modified residue
MA6	D	A	modified residue
OMC	Y	C	modified residue
OMG	Y	G	modified residue
OMU	Y	U	modified residue
PSU	D	U	modified residue
UR3	D	U	modified residue

Ligand Molecules

Primary Citation

Ribosome rearrangements at the onset of translational bypassing.

Agirrezabala, X, Samatova, E, Klimova, M, Zamora, M, Gil-Carton, D, Rodnina, M.V, Valle, M.Show

Sci Adv 3 e1700147 e1700147 (2017)

PMID: 28630923 DOI: 10.1126/sciadv.1700147

Abstact

Bypassing is a recoding event that leads to the translation of two distal open reading frames into a single polypeptide chain. We present the structure of a translating ribosome stalled at the bypassing take-off site of gene 60 of bacteriophage T4. The nascent peptide in the exit tunnel anchors the P-site peptidyl-tRNAGly to the ribosome and locks an inactive conformation of the peptidyl transferase center (PTC). The mRNA forms a short dynamic hairpin in the decoding site. The ribosomal subunits adopt a rolling conformation in which the rotation of the small subunit around its long axis causes the opening of the A-site region. Together, PTC conformation and mRNA structure safeguard against premature termination and read-through of the stop codon and reconfigure the ribosome to a state poised for take-off and sliding along the noncoding mRNA gap.

Legend

Protein

Chemical

Disease

Primary Citation of related structures

Abstact

Feedback Form