ISDA

Deposition Date 2020-02-27

Release Date 2020-09-02

Last Version Date 2024-10-09

Entry Detail

PDB ID:

6VYX

Keywords:

Ribosome/transcription/translation

Title:

Escherichia coli transcription-translation complex C4 (TTC-C4) containing mRNA with a 21 nt long spacer, transcription factor NusG, and fMet-tRNAs at P-site and E-site

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

9.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:A (auth: 0)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG48 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:B (auth: 1)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:C (auth: 2)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:D (auth: 3)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:E (auth: 4)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68919 Pfam ID:PF01386

Polymer Type:polydeoxyribonucleotide
Molecule:NT DNA
Chain IDs:F (auth: 5)
Chain Length:27
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:T DNA
Chain IDs:G (auth: 6)
Chain Length:27
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:mRNA with 21 nt long spacer
Chain IDs:H (auth: 7)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:E-site and P-site tRNA (fMet)
Chain IDs:I (auth: A), P (auth: B)
Chain Length:2904
Number of Molecules:2
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Chain IDs:J (auth: AA)
Chain Length:1342
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A8V2 Pfam ID:PF04563, PF04561, PF04565, PF10385, PF00562, PF04560

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription termination/antitermination protein NusG
Chain IDs:K (auth: AB)
Chain Length:181
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AFG0 Pfam ID:PF02357, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Chain IDs:L (auth: AC), M (auth: AD)
Chain Length:329
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7Z4 Pfam ID:PF01193, PF01000, PF03118

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Chain IDs:N (auth: AE)
Chain Length:1407
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A8T7 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Chain IDs:O (auth: AF)
Chain Length:91
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A800 Pfam ID:PF01192

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:Q (auth: C)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T7 Pfam ID:PF01084

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:R (auth: D)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:S (auth: E)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U7 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:T (auth: F)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68679 Pfam ID:PF01165

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:U (auth: G)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V0 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S1
Chain IDs:V (auth: H)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG67 Pfam ID:PF00575

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:W (auth: I)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:X (auth: J)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:Y (auth: K)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:Z (auth: L)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02358 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:AA (auth: M)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:BA (auth: N)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W7 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:CA (auth: O)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7X3 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:DA (auth: P)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R5 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:EA (auth: Q)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R9 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:FA (auth: R)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:GA (auth: S)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG59 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:HA (auth: T)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ4 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:IA (auth: U)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:JA (auth: V)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG63 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:KA (auth: W)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U3 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:LA (auth: X)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S9 Pfam ID:PF00416

Polymer Type:polyribonucleotide
Molecule:mRNA in the ribosomal RNA entrance pore
Chain IDs:MA (auth: Y)
Chain Length:115
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:NA (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:OA (auth: b)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L8 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:PA (auth: c)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M2 Pfam ID:PF00830

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:QA (auth: d)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:RA (auth: e)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:SA (auth: f)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG51 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:TA (auth: g)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M9 Pfam ID:PF01197

Protein Blast

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

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:VA (auth: i)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N4 Pfam ID:PF01783

Protein Blast

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

UniProt ID:P60438 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:XA (auth: k)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N9 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:YA (auth: l)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:ZA (auth: m)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7P5 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:AB (auth: n)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:BB (auth: o)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:CB (auth: p)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG55 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:DB (auth: q)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:EB (auth: r)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:FB (auth: s)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AA10 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:GB (auth: t)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY3 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:HB (auth: u)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02413 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:IB (auth: v)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY7 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:JB (auth: w)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG44 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:KB (auth: x)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0C018 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:LB (auth: y)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7K6 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:MB (auth: z)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L3 Pfam ID:PF00453

Ligand Molecules

Primary Citation

Structural basis of transcription-translation coupling.

Wang, C, Molodtsov, V, Firlar, E, Kaelber, J.T, Blaha, G, Su, M, Ebright, R.H.Show

Science 369 1359 1365 (2020)

PMID: 32820061 DOI: 10.1126/science.abb5317

Abstact

In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA. Here, we report cryo-electron microscopy structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A, previously termed "expressome"). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.

Legend

Protein

Chemical

Disease

Primary Citation of related structures