ISDA

Deposition Date 2021-03-29

Release Date 2021-09-01

Last Version Date 2025-03-12

Entry Detail

PDB ID:

7O1A

Keywords:

TRANSLATION

Title:

Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan

Biological Source:

Source Organism:

Escherichia coli K-12 (Taxon ID: 83333)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 16S
Chain IDs:A (auth: AA)
Chain Length:1534
Number of Molecules:1
Biological Source:Escherichia coli K-12

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB)
Chain Length:240
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V0 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02358 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02359 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: AH)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W7 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7X3 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R5 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R9 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S9 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:N (auth: AN)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG59 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ4 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7T3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: AQ)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG63 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T7 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U3 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U7 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P68679 Pfam ID:PF01165

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:VA (auth: B0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N4 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:WA (auth: B1)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N9 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:XA (auth: B2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7P5 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:YA (auth: B3)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7Q1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:ZA (auth: B4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7Q6 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TnaC - Tryptophanase leader peptide - R23F
Chain IDs:AB (auth: B5)
Chain Length:17
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AD89 Pfam ID:PF08053

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:BB (auth: B7)
Chain Length:9
Number of Molecules:1
Biological Source:Escherichia coli K-12

Polymer Type:polyribonucleotide
Molecule:P-site tRNA-Pro
Chain IDs:CB (auth: B8)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 23S
Chain IDs:V (auth: BA)
Chain Length:2897
Number of Molecules:1
Biological Source:Escherichia coli K-12

Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 5S
Chain IDs:W (auth: BB)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli K-12

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:X (auth: BC)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:Y (auth: BD)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60438 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:Z (auth: BE)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P60723 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:AA (auth: BF)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:BA (auth: BG)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG55 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:CA (auth: BH)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:DA (auth: BI)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M9 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:EA (auth: BJ)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AA10 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:FA (auth: BK)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0ADY3 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:GA (auth: BL)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P02413 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:HA (auth: BM)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0ADY7 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:IA (auth: BN)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG44 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:JA (auth: BO)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0C018 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:KA (auth: BP)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7K6 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:LA (auth: BQ)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L3 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:MA (auth: BR)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P0AG48 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:NA (auth: BS)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P61175 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:OA (auth: BT)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:PA (auth: BU)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:QA (auth: BV)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P68919 Pfam ID:PF01386

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:RA (auth: BW)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L8 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:SA (auth: BX)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M2 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:TA (auth: BY)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:UA (auth: BZ)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG51 Pfam ID:PF00327

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
1MG	CB	G	modified residue
2MG	A	G	modified residue
4D4	HA	ARG	modified residue
4OC	A	C	modified residue
5MC	A	C	modified residue
D2T	L	ASP	modified residue
G7M	A	G	modified residue
MA6	A	A	modified residue
MEQ	Y	GLN	modified residue
PSU	A	U	modified residue
UR3	A	U	modified residue

Ligand Molecules

TRP

Primary Citation

Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling.

van der Stel, A.X, Gordon, E.R, Sengupta, A, Martinez, A.K, Klepacki, D, Perry, T.N, Herrero Del Valle, A, Vazquez-Laslop, N, Sachs, M.S, Cruz-Vera, L.R, Innis, C.A.Show

Nat Commun 12 5340 5340 (2021)

PMID: 34504068 DOI: 10.1038/s41467-021-25663-8

Abstact

Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC-ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.

Legend

Protein

Chemical

Disease

Primary Citation of related structures