6X6T

Cryo-EM structure of an Escherichia coli coupled transcription-translation complex B1 (TTC-B1) containing an mRNA with a 24 nt long spacer, transcription factors NusA and NusG, and fMet-tRNAs at P-site and E-site


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcription-translation coupling.

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

(2020) Science 369: 1359-1365

  • DOI: 10.1126/science.abb5317
  • Primary Citation of Related Structures:  
    6X7F, 6X7K, 6X6T, 6X9Q, 6XDR, 6XDQ, 6XGF, 6XIJ, 6XII, 6VU3, 6VYR, 6VZ3, 6VYQ, 6VZ2, 6VYT, 6VZ5, 6VYS, 6VZ7, 6VYU, 6VYX, 6VYW, 6VZJ, 6VYZ, 6VYY

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. minsu@umich.edu ebright@waksman.rutgers.edu.



Macromolecules

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Entity ID: 1
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50S ribosomal protein L21A [auth 0]103Escherichia coliMutation(s): 0 
Gene Names: rplU
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50S ribosomal protein L22B [auth 1]110Escherichia coliMutation(s): 0 
Gene Names: rplV
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50S ribosomal protein L23C [auth 2]100Escherichia coliMutation(s): 0 
Gene Names: rplW
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50S ribosomal protein L24D [auth 3]104Escherichia coliMutation(s): 0 
Gene Names: rplX
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Entity ID: 5
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50S ribosomal protein L25E [auth 4]94Escherichia coliMutation(s): 0 
Gene Names: rplY
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50S ribosomal protein L10I [auth 9]165Escherichia coliMutation(s): 0 
Gene Names: rplJ
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Entity ID: 11
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DNA-directed RNA polymerase subunit betaK [auth AA]1342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
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Entity ID: 12
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Transcription termination/antitermination protein NusGL [auth AB]181Escherichia coliMutation(s): 0 
Gene Names: nusG
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DNA-directed RNA polymerase subunit alphaM [auth AC], N [auth AD]329Escherichia coliMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
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DNA-directed RNA polymerase subunit beta'O [auth AE]1407Escherichia coliMutation(s): 1 
Gene Names: rpoCBvCmsKKP036_03580G5696_22040
EC: 2.7.7.6
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DNA-directed RNA polymerase subunit omegaP [auth AF]91Escherichia coliMutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
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Transcription termination/antitermination protein NusAQ [auth AG]495Escherichia coliMutation(s): 0 
Gene Names: nusA
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30S ribosomal protein S18S [auth C]75Escherichia coliMutation(s): 0 
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30S ribosomal protein S20U [auth E]87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21V [auth F]71Escherichia coliMutation(s): 0 
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30S ribosomal protein S2W [auth G]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S1X [auth H]557Escherichia coliMutation(s): 0 
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30S ribosomal protein S3Y [auth I]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4Z [auth J]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5AA [auth K]167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6BA [auth L]135Escherichia coliMutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S7CA [auth M]179Escherichia coliMutation(s): 0 
Gene Names: rpsGGHR40_06850NCTC12650_00665
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30S ribosomal protein S8DA [auth N]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S9EA [auth O]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10FA [auth P]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11GA [auth Q]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12HA [auth R]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S14IA [auth S]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15JA [auth T]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16KA [auth U]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17LA [auth V]84Escherichia coliMutation(s): 0 
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30S ribosomal protein S19MA [auth W]92Escherichia coliMutation(s): 0 
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30S ribosomal protein S13NA [auth X]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L11OA [auth Y]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L7/L12PA [auth Z]121Escherichia coliMutation(s): 0 
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50S ribosomal protein L27RA [auth b]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28SA [auth c]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29UA [auth e]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30VA [auth f]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L31WA [auth g]70Escherichia coliMutation(s): 0 
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50S ribosomal protein L2XA [auth h]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L32YA [auth i]57Escherichia coliMutation(s): 0 
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50S ribosomal protein L3ZA [auth j]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L33AB [auth k]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L4BB [auth l]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L34CB [auth m]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L5DB [auth n]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L35EB [auth o]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L6FB [auth p]177Escherichia coliMutation(s): 0 
Gene Names: rplF
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50S ribosomal protein L36GB [auth q]38Escherichia coliMutation(s): 0 
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50S ribosomal protein L9HB [auth r]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L13IB [auth s]142Escherichia coliMutation(s): 0 
Gene Names: rplM
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50S ribosomal protein L14JB [auth t]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15KB [auth u]144Escherichia coliMutation(s): 0 
Gene Names: 
rplOA8C65_19395A9R57_24660ACU57_21045AM464_09135AUQ13_22145BANRA_01932BANRA_03684BHS87_18545BJJ90_02210BMA87_18510BON75_18850BON98_13310BUE81_25610BvCms2454_01416BvCmsHHP001_00334BvCmsHHP019_04131BvCmsHHP056_02703BvCmsKSP026_02554BvCmsSINP011_02480BW690_10710BZL31_22885C5F72_02595C5F73_02860C5N07_23575C9E25_20065C9Z39_20710CA593_09735CG692_20270CI693_13520CI694_01990CIG45_22410D0X26_24495D2185_22985D3821_17755D3O91_20305D3Y67_24390D4638_19455D4718_17880D9C99_17930D9D20_21995D9D44_22490D9G29_15635D9G69_20945D9H68_17710D9J52_19090D9Z28_15390DAH37_14685DBQ99_03415DJ503_19770DL326_22310DNC98_19095DT034_22410DTL43_21000E2119_19640E2134_21880E2135_06185E4A44_21305E4K51_21490E4K55_21420E4K60_18985E4K61_20025E5P22_10480E5P28_20875EA213_19860EAI42_04990EAI52_16365EC1094V2_354EC3234A_55c00230EC3426_04459ECTO6_00449ED307_17010EEP23_17135EG808_17075EI021_21030EI028_20740EI032_18995EI041_20035EIZ93_12470EL75_0396EL79_0415EL80_0407ELT20_19170EPT01_19765ERS085365_03907ERS085416_03881ERS139211_03685ERS150873_04051EXX71_21335EYD11_02080F1E19_19655F9040_18095FRV13_20015FV293_22465FWK02_06270G5632_17770G5688_20025GHR40_07050GKF39_20550GKF74_18130GKF86_20070GKF89_18470GP671_20580GP689_20785GP954_00945GP979_02005GQE33_22230GQE34_14255GQE64_20420GQM17_19915GRW05_09060GRW27_21285GRW42_19350GRW57_03540GRW80_20585GRW81_21150NCTC10963_00456NCTC11022_03475NCTC11126_02772NCTC12650_00710NCTC13216_01351NCTC9045_00567NCTC9062_02686NCTC9117_00757NCTC9706_02738PGD_00585RK56_021420SAMEA3472047_03862SAMEA3472080_04748SAMEA3484427_04887SAMEA3484429_04875SAMEA3752559_00346SAMEA3753300_02227

UniProt
Find proteins for A0A037Y8L6 (Escherichia coli)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16LB [auth v]136Escherichia coliMutation(s): 0 
Gene Names: rplPb3313JW3275
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17MB [auth w]127Escherichia coliMutation(s): 0 
Gene Names: rplQECCG_03701
UniProt
Find proteins for D6I1Y5 (Escherichia coli B088)
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18NB [auth x]117Escherichia coliMutation(s): 0 
Gene Names: rplR
UniProt
Find proteins for D7Z9H1 (Escherichia coli MS 69-1)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19OB [auth y]115Escherichia coliMutation(s): 0 
Gene Names: rplS
UniProt
Find proteins for D7ZKU3 (Escherichia coli MS 69-1)
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20PB [auth z]118Escherichia coliMutation(s): 0 
Gene Names: rplT
UniProt
Find proteins for B7MAS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 6
MoleculeChainsLengthOrganismImage
NT DNAF [auth 5]36synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
T DNAG [auth 6]36synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
mRNA with 24 nt long spacerH [auth 7]41synthetic construct
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Entity ID: 10
MoleculeChainsLengthOrganismImage
E-site and P-site tRNA (fMet)J [auth A], R [auth B]76Escherichia coli
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Entity ID: 18
MoleculeChainsLengthOrganismImage
16S rRNAT [auth D]1542Escherichia coli
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Entity ID: 41
MoleculeChainsLengthOrganismImage
23S rRNAQA [auth a]2904Escherichia coli
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Entity ID: 44
MoleculeChainsLengthOrganismImage
5S rRNATA [auth d]120Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
RB [auth AA], SB [auth AA]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
QB [auth 7]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references