6ZTN

E. coli 70S-RNAP expressome complex in NusG-coupled state (42 nt intervening mRNA)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of transcription-translation coupling and collision in bacteria.

Webster, M.W., Takacs, M., Zhu, C., Vidmar, V., Eduljee, A., Abdelkareem, M., Weixlbaumer, A.

(2020) Science 369: 1355-1359

  • DOI: https://doi.org/10.1126/science.abb5036
  • Primary Citation of Related Structures:  
    6ZTJ, 6ZTL, 6ZTM, 6ZTN, 6ZTO, 6ZTP, 6ZU1

  • PubMed Abstract: 

    Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo-electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.

    • Organizational Affiliation: 

    Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB]241Escherichia coliMutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S3C [auth AC]233Escherichia coliMutation(s): 0 
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Entity ID: 4
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30S ribosomal protein S4D [auth AD]206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE]167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF]131Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG]156Escherichia coliMutation(s): 0 
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30S ribosomal protein S8H [auth AH]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S9I [auth AI]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10J [auth AJ]103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11K [auth AK]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12L [auth AL]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13M [auth AM]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14N [auth AN]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15O [auth AO]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16P [auth AP]82Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ]84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18R [auth AR]75Escherichia coliMutation(s): 0 
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Entity ID: 19
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30S ribosomal protein S19S [auth AS]92Escherichia coliMutation(s): 0 
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Entity ID: 20
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30S ribosomal protein S20T [auth AT]87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21U [auth AU]71Escherichia coliMutation(s): 0 
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50S ribosomal protein L2BA [auth BC]273Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L3CA [auth BD]209Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L4DA [auth BE]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5EA [auth BF]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6FA [auth BG]177Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L9GA [auth BH]149Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L13HA [auth BK]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14IA [auth BL]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15JA [auth BM]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16KA [auth BN]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17LA [auth BO]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18MA [auth BP]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19NA [auth BQ]115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20OA [auth BR]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21PA [auth BS]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22QA [auth BT]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23RA [auth BU]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24SA [auth BV]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25TA [auth BW]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27UA [auth BX]85Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28VA [auth BY]78Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth BZ]63Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth B1]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L32YA [auth B2]57Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33ZA [auth B3]55Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth B4]46Escherichia coliMutation(s): 0 
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UniProt GroupP0A7P5
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth B5]65Escherichia coliMutation(s): 0 
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UniProt GroupP0A7Q1
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth B6]50Escherichia coliMutation(s): 0 
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UniProt GroupP0A7Q6
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaDB [auth CA],
EB [auth CB]		329Escherichia coliMutation(s): 0 
Gene Names: rpoA, pez, phs, sez, b3295, JW3257
EC: 2.7.7.6
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaFB [auth CC]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoB, Z5560, ECs4910
EC: 2.7.7.6
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'GB [auth CD]1,407Escherichia coliMutation(s): 0 
Gene Names: rpoC, Z5561, ECs4911
EC: 2.7.7.6
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaHB [auth CE]91Escherichia coliMutation(s): 0 
Gene Names: rpoZ, b3649, JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusGKB [auth CF]181Escherichia coliMutation(s): 0 
Gene Names: nusG
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA]1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
mRNAV [auth AV]57synthetic construct
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Entity ID: 23
MoleculeChains LengthOrganismImage
tRNA(fmet) P-siteW [auth AW]77Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
Phe-NH-tRNA(Phe) A-siteX [auth AX],
Y [auth AZ]		76Escherichia coli
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S ribosomal RNAZ [auth BA]2,904Escherichia coli
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S ribosomal RNAAA [auth BB]120Escherichia coli
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Entity ID: 59
MoleculeChains LengthOrganismImage
Non-template DNA strandIB [auth CN]39synthetic construct
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Entity ID: 60
MoleculeChains LengthOrganismImage
Template DNA strandJB [auth CT]39synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE
Download Ideal Coordinates CCD File 
EH [auth AX]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
FU [auth CD],
GU [auth CD]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth AA]
AD [auth AA]
AE [auth AA]
AF [auth AA]
AG [auth AA]
AC [auth AA],
AD [auth AA],
AE [auth AA],
AF [auth AA],
AG [auth AA],
AH [auth AW],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AL [auth BA],
AM [auth BA],
AN [auth BA],
AO [auth BA],
AP [auth BA],
AQ [auth BA],
AR [auth BA],
AS [auth BA],
AT [auth BA],
AU [auth BX],
BC [auth AA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth AA],
BH [auth AW],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth BA],
BM [auth BA],
BN [auth BA],
BO [auth BA],
BP [auth BA],
BQ [auth BA],
BR [auth BA],
BS [auth BA],
BT [auth BA],
BU [auth B2],
CC [auth AA],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CG [auth AA],
CH [auth AW],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth BA],
CM [auth BA],
CN [auth BA],
CO [auth BA],
CP [auth BA],
CQ [auth BA],
CR [auth BA],
CS [auth BA],
CT [auth BA],
CU [auth B5],
DC [auth AA],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DG [auth AA],
DH [auth AX],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth BA],
DM [auth BA],
DN [auth BA],
DO [auth BA],
DP [auth BA],
DQ [auth BA],
DR [auth BA],
DS [auth BA],
DT [auth BA],
DU [auth B6],
EC [auth AA],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EG [auth AA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth BA],
EM [auth BA],
EN [auth BA],
EO [auth BA],
EP [auth BA],
EQ [auth BA],
ER [auth BA],
ES [auth BA],
ET [auth BA],
EU [auth CD],
FC [auth AA],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FG [auth AA],
FH [auth BA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth BA],
FM [auth BA],
FN [auth BA],
FO [auth BA],
FP [auth BA],
FQ [auth BA],
FR [auth BA],
FS [auth BA],
FT [auth BA],
GC [auth AA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GG [auth AA],
GH [auth BA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth BA],
GM [auth BA],
GN [auth BA],
GO [auth BA],
GP [auth BA],
GQ [auth BA],
GR [auth BA],
GS [auth BA],
GT [auth BA],
HC [auth AA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth AA],
HH [auth BA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth BA],
HM [auth BA],
HN [auth BA],
HO [auth BA],
HP [auth BA],
HQ [auth BA],
HR [auth BA],
HS [auth BA],
HT [auth BA],
IC [auth AA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth AA],
IH [auth BA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth BA],
IM [auth BA],
IN [auth BA],
IO [auth BA],
IP [auth BA],
IQ [auth BA],
IR [auth BA],
IS [auth BA],
IT [auth BA],
JC [auth AA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth AA],
JH [auth BA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth BA],
JM [auth BA],
JN [auth BA],
JO [auth BA],
JP [auth BA],
JQ [auth BA],
JR [auth BA],
JS [auth BA],
JT [auth BA],
KC [auth AA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth AA],
KH [auth BA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth BA],
KM [auth BA],
KN [auth BA],
KO [auth BA],
KP [auth BA],
KQ [auth BA],
KR [auth BA],
KS [auth BA],
KT [auth BA],
LB [auth AA],
LC [auth AA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth AA],
LH [auth BA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth BA],
LM [auth BA],
LN [auth BA],
LO [auth BA],
LP [auth BA],
LQ [auth BA],
LR [auth BA],
LS [auth BA],
LT [auth BB],
MB [auth AA],
MC [auth AA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth AA],
MH [auth BA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth BA],
MM [auth BA],
MN [auth BA],
MO [auth BA],
MP [auth BA],
MQ [auth BA],
MR [auth BA],
MS [auth BA],
MT [auth BB],
NB [auth AA],
NC [auth AA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth AA],
NH [auth BA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth BA],
NM [auth BA],
NN [auth BA],
NO [auth BA],
NP [auth BA],
NQ [auth BA],
NR [auth BA],
NS [auth BA],
NT [auth BB],
OB [auth AA],
OC [auth AA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth AA],
OH [auth BA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth BA],
OM [auth BA],
ON [auth BA],
OO [auth BA],
OP [auth BA],
OQ [auth BA],
OR [auth BA],
OS [auth BA],
OT [auth BB],
PB [auth AA],
PC [auth AA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth AA],
PH [auth BA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth BA],
PM [auth BA],
PN [auth BA],
PO [auth BA],
PP [auth BA],
PQ [auth BA],
PR [auth BA],
PS [auth BA],
PT [auth BB],
QB [auth AA],
QC [auth AA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth AA],
QH [auth BA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth BA],
QM [auth BA],
QN [auth BA],
QO [auth BA],
QP [auth BA],
QQ [auth BA],
QR [auth BA],
QS [auth BA],
QT [auth BB],
RB [auth AA],
RC [auth AA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth AA],
RH [auth BA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth BA],
RM [auth BA],
RN [auth BA],
RO [auth BA],
RP [auth BA],
RQ [auth BA],
RR [auth BA],
RS [auth BA],
RT [auth BB],
SB [auth AA],
SC [auth AA],
SD [auth AA],
SE [auth AA],
SF [auth AA],
SG [auth AA],
SH [auth BA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth BA],
SM [auth BA],
SN [auth BA],
SO [auth BA],
SP [auth BA],
SQ [auth BA],
SR [auth BA],
SS [auth BA],
ST [auth BB],
TB [auth AA],
TC [auth AA],
TD [auth AA],
TE [auth AA],
TF [auth AA],
TG [auth AA],
TH [auth BA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth BA],
TM [auth BA],
TN [auth BA],
TO [auth BA],
TP [auth BA],
TQ [auth BA],
TR [auth BA],
TS [auth BA],
TT [auth BB],
UB [auth AA],
UC [auth AA],
UD [auth AA],
UE [auth AA],
UF [auth AA],
UG [auth AL],
UH [auth BA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth BA],
UM [auth BA],
UN [auth BA],
UO [auth BA],
UP [auth BA],
UQ [auth BA],
UR [auth BA],
US [auth BA],
UT [auth BC],
VB [auth AA],
VC [auth AA],
VD [auth AA],
VE [auth AA],
VF [auth AA],
VG [auth AL],
VH [auth BA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth BA],
VM [auth BA],
VN [auth BA],
VO [auth BA],
VP [auth BA],
VQ [auth BA],
VR [auth BA],
VS [auth BA],
VT [auth BC],
WB [auth AA],
WC [auth AA],
WD [auth AA],
WE [auth AA],
WF [auth AA],
WG [auth AL],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth BA],
WM [auth BA],
WN [auth BA],
WO [auth BA],
WP [auth BA],
WQ [auth BA],
WR [auth BA],
WS [auth BA],
WT [auth BC],
XB [auth AA],
XC [auth AA],
XD [auth AA],
XE [auth AA],
XF [auth AA],
XG [auth AT],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XK [auth BA],
XL [auth BA],
XM [auth BA],
XN [auth BA],
XO [auth BA],
XP [auth BA],
XQ [auth BA],
XR [auth BA],
XS [auth BA],
XT [auth BD],
YB [auth AA],
YC [auth AA],
YD [auth AA],
YE [auth AA],
YF [auth AA],
YG [auth AV],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YK [auth BA],
YL [auth BA],
YM [auth BA],
YN [auth BA],
YO [auth BA],
YP [auth BA],
YQ [auth BA],
YR [auth BA],
YS [auth BA],
YT [auth BN],
ZB [auth AA],
ZC [auth AA],
ZD [auth AA],
ZE [auth AA],
ZF [auth AA],
ZG [auth AW],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZK [auth BA],
ZL [auth BA],
ZM [auth BA],
ZN [auth BA],
ZO [auth BA],
ZP [auth BA],
ZQ [auth BA],
ZR [auth BA],
ZS [auth BA],
ZT [auth BR]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T		L [auth AL]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ		CA [auth BD]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		KA [auth BN]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16
RECONSTRUCTIONRELION3.0.4

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)France679734
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05
French National Research AgencyFranceANR-10-LABX-0030-INRT
French National Research AgencyFranceANR-10-IDEX-0002-02
European Molecular Biology Organization (EMBO)FranceLTF375-2019

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2024-04-24
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary