8PEG

Escherichia coli paused disome complex (queueing 70S non-rotated closed PRE state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM.

Flugel, T.Schacherl, M.Unbehaun, A.Schroeer, B.Dabrowski, M.Burger, J.Mielke, T.Sprink, T.Diebolder, C.A.Guillen Schlippe, Y.V.Spahn, C.M.T.

(2024) Nat Commun 15: 1756-1756

  • DOI: https://doi.org/10.1038/s41467-024-46092-3
  • Primary Citation of Related Structures:  
    8PEG, 8PKL, 8R3V, 8RCL, 8RCM, 8RCS, 8RCT

  • PubMed Abstract: 

    Structural studies of translating ribosomes traditionally rely on in vitro assembly and stalling of ribosomes in defined states. To comprehensively visualize bacterial translation, we reactivated ex vivo-derived E. coli polysomes in the PURE in vitro translation system and analyzed the actively elongating polysomes by cryo-EM. We find that 31% of 70S ribosomes assemble into disome complexes that represent eight distinct functional states including decoding and termination intermediates, and a pre-nucleophilic attack state. The functional diversity of disome complexes together with RNase digest experiments suggests that paused disome complexes transiently form during ongoing elongation. Structural analysis revealed five disome interfaces between leading and queueing ribosomes that undergo rearrangements as the leading ribosome traverses through the elongation cycle. Our findings reveal at the molecular level how bL9's CTD obstructs the factor binding site of queueing ribosomes to thwart harmful collisions and illustrate how translation dynamics reshape inter-ribosomal contacts.


  • Organizational Affiliation

    Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36A [auth 0]38Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28B [auth 1]78Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29C [auth 2]63Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30D [auth 3]59Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31AE [auth 4]70Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32F [auth 5]57Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35G [auth 6]65Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2K [auth B]241Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3L [auth C]233Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4M [auth D]206Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5N [auth E]167Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6O [auth F]135Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7P [auth G]179Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8Q [auth H]130Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9R [auth I]130Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10S [auth J]103Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11T [auth K]129Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12U [auth L]124Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13V [auth M]118Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14W [auth N]101Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15X [auth O]89Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16Y [auth P]82Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17Z [auth Q]84Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18AA [auth R]75Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19BA [auth S]92Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20CA [auth T]87Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21DA [auth U]71Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1IA [auth Z]557Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1JA [auth a]234Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2KA [auth b]273Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3LA [auth c]209Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4MA [auth d]201Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5NA [auth e]179Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6OA [auth f]177Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33PA [auth g]55Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16QA [auth h]136Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9RA [auth i]149Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10SA [auth j]165Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11TA [auth k]142Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34UA [auth l]46Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13VA [auth m]142Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14WA [auth n]123Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15XA [auth o]144Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainYA [auth p]18Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17ZA [auth q]127Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18AB [auth r]117Escherichia coliMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19BB [auth s]115Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20CB [auth t]118Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21DB [auth u]103Escherichia coliMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22EB [auth v]110Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23FB [auth w]100Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24GB [auth x]104Escherichia coliMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25HB [auth y]94Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27IB [auth z]85Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains LengthOrganismImage
23S ribosomal RNAH [auth 7]2,903Escherichia coli
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S ribosomal RNAI [auth 8]120Escherichia coli
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Entity ID: 10
MoleculeChains LengthOrganismImage
16S ribosomal RNAJ [auth A]1,542Escherichia coli
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Entity ID: 31
MoleculeChains LengthOrganismImage
mRNAEA [auth V]30Escherichia coli
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Entity ID: 32
MoleculeChains LengthOrganismImage
tRNA-Phe (P-site)FA [auth W]76Escherichia coli
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Entity ID: 33
MoleculeChains LengthOrganismImage
tRNA-Ser (E-site)GA [auth X]78Escherichia coli
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Entity ID: 34
MoleculeChains LengthOrganismImage
tRNA-Val (A-site)HA [auth Y]76Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
VI [auth 7],
WI [auth 7]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JB [auth 0],
KB [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth 7]
AD [auth 7]
AE [auth 7]
AF [auth 7]
AG [auth 7]
AC [auth 7],
AD [auth 7],
AE [auth 7],
AF [auth 7],
AG [auth 7],
AH [auth 7],
AI [auth 7],
AJ [auth A],
AK [auth A],
AL [auth A],
BC [auth 7],
BD [auth 7],
BE [auth 7],
BF [auth 7],
BG [auth 7],
BH [auth 7],
BI [auth 7],
BJ [auth A],
BK [auth A],
BL [auth A],
CC [auth 7],
CD [auth 7],
CE [auth 7],
CF [auth 7],
CG [auth 7],
CH [auth 7],
CI [auth 7],
CJ [auth A],
CK [auth A],
CL [auth A],
DC [auth 7],
DD [auth 7],
DE [auth 7],
DF [auth 7],
DG [auth 7],
DH [auth 7],
DI [auth 7],
DJ [auth A],
DK [auth A],
DL [auth A],
EC [auth 7],
ED [auth 7],
EE [auth 7],
EF [auth 7],
EG [auth 7],
EH [auth 7],
EI [auth 7],
EJ [auth A],
EK [auth A],
EL [auth A],
FC [auth 7],
FD [auth 7],
FE [auth 7],
FF [auth 7],
FG [auth 7],
FH [auth 7],
FI [auth 7],
FJ [auth A],
FK [auth A],
FL [auth A],
GC [auth 7],
GD [auth 7],
GE [auth 7],
GF [auth 7],
GG [auth 7],
GH [auth 7],
GI [auth 7],
GJ [auth A],
GK [auth A],
GL [auth A],
HC [auth 7],
HD [auth 7],
HE [auth 7],
HF [auth 7],
HG [auth 7],
HH [auth 7],
HI [auth 7],
HJ [auth A],
HK [auth A],
HL [auth A],
IC [auth 7],
ID [auth 7],
IE [auth 7],
IF [auth 7],
IG [auth 7],
IH [auth 7],
II [auth 7],
IJ [auth A],
IK [auth A],
IL [auth A],
JC [auth 7],
JD [auth 7],
JE [auth 7],
JF [auth 7],
JG [auth 7],
JH [auth 7],
JI [auth 7],
JJ [auth A],
JK [auth A],
JL [auth X],
KC [auth 7],
KD [auth 7],
KE [auth 7],
KF [auth 7],
KG [auth 7],
KH [auth 7],
KI [auth 7],
KJ [auth A],
KK [auth A],
KL [auth Y],
LB [auth 7],
LC [auth 7],
LD [auth 7],
LE [auth 7],
LF [auth 7],
LG [auth 7],
LH [auth 7],
LI [auth 7],
LJ [auth A],
LK [auth A],
LL [auth b],
MB [auth 7],
MC [auth 7],
MD [auth 7],
ME [auth 7],
MF [auth 7],
MG [auth 7],
MH [auth 7],
MI [auth 7],
MJ [auth A],
MK [auth A],
ML [auth o],
NB [auth 7],
NC [auth 7],
ND [auth 7],
NE [auth 7],
NF [auth 7],
NG [auth 7],
NH [auth 7],
NI [auth 7],
NJ [auth A],
NK [auth A],
OB [auth 7],
OC [auth 7],
OD [auth 7],
OE [auth 7],
OF [auth 7],
OG [auth 7],
OH [auth 7],
OI [auth 7],
OJ [auth A],
OK [auth A],
PB [auth 7],
PC [auth 7],
PD [auth 7],
PE [auth 7],
PF [auth 7],
PG [auth 7],
PH [auth 7],
PI [auth 7],
PJ [auth A],
PK [auth A],
QB [auth 7],
QC [auth 7],
QD [auth 7],
QE [auth 7],
QF [auth 7],
QG [auth 7],
QH [auth 7],
QI [auth 7],
QJ [auth A],
QK [auth A],
RB [auth 7],
RC [auth 7],
RD [auth 7],
RE [auth 7],
RF [auth 7],
RG [auth 7],
RH [auth 7],
RI [auth 7],
RJ [auth A],
RK [auth A],
SB [auth 7],
SC [auth 7],
SD [auth 7],
SE [auth 7],
SF [auth 7],
SG [auth 7],
SH [auth 7],
SI [auth 7],
SJ [auth A],
SK [auth A],
TB [auth 7],
TC [auth 7],
TD [auth 7],
TE [auth 7],
TF [auth 7],
TG [auth 7],
TH [auth 7],
TI [auth 7],
TJ [auth A],
TK [auth A],
UB [auth 7],
UC [auth 7],
UD [auth 7],
UE [auth 7],
UF [auth 7],
UG [auth 7],
UH [auth 7],
UI [auth 7],
UJ [auth A],
UK [auth A],
VB [auth 7],
VC [auth 7],
VD [auth 7],
VE [auth 7],
VF [auth 7],
VG [auth 7],
VH [auth 7],
VJ [auth A],
VK [auth A],
WB [auth 7],
WC [auth 7],
WD [auth 7],
WE [auth 7],
WF [auth 7],
WG [auth 7],
WH [auth 7],
WJ [auth A],
WK [auth A],
XB [auth 7],
XC [auth 7],
XD [auth 7],
XE [auth 7],
XF [auth 7],
XG [auth 7],
XH [auth 7],
XI [auth 7],
XJ [auth A],
XK [auth A],
YB [auth 7],
YC [auth 7],
YD [auth 7],
YE [auth 7],
YF [auth 7],
YG [auth 7],
YH [auth 7],
YI [auth A],
YJ [auth A],
YK [auth A],
ZB [auth 7],
ZC [auth 7],
ZD [auth 7],
ZE [auth 7],
ZF [auth 7],
ZG [auth 7],
ZH [auth 7],
ZI [auth A],
ZJ [auth A],
ZK [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Data collection