8B0X

Translating 70S ribosome in the unrotated state (P and E, tRNAs)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The translating bacterial ribosome at 1.55 angstrom resolution generated by cryo-EM imaging services.

Fromm, S.A.O'Connor, K.M.Purdy, M.Bhatt, P.R.Loughran, G.Atkins, J.F.Jomaa, A.Mattei, S.

(2023) Nat Commun 14: 1095-1095

  • DOI: https://doi.org/10.1038/s41467-023-36742-3
  • Primary Citation of Related Structures:  
    8B0X

  • PubMed Abstract: 

    Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance.


  • Organizational Affiliation

    EMBL Imaging Centre, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33A [auth 0]55Escherichia coli BMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 1]46Escherichia coli BMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35C [auth 2]65Escherichia coli BMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36D [auth 3]38Escherichia coli BMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2F [auth B]241Escherichia coli BMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3G [auth C]233Escherichia coli BMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4H [auth D]206Escherichia coli BMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5I [auth E]167Escherichia coli BMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6J [auth F]135Escherichia coli BMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7K [auth G]179Escherichia coli BMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8L [auth H]130Escherichia coli BMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9M [auth I]130Escherichia coli BMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10N [auth J]103Escherichia coli BMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11O [auth K]129Escherichia coli BMutation(s): 1 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12P [auth L]124Escherichia coli BMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13Q [auth M]118Escherichia coli BMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14R [auth N]101Escherichia coli BMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15S [auth O]89Escherichia coli BMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16T [auth P]82Escherichia coli BMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17U [auth Q]84Escherichia coli BMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18V [auth R]75Escherichia coli BMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19W [auth S]92Escherichia coli BMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20X [auth T]87Escherichia coli BMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21Y [auth U]71Escherichia coli BMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2DA [auth c]273Escherichia coli BMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3EA [auth d]209Escherichia coli BMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L4FA [auth e]201Escherichia coli BMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5GA [auth f]179Escherichia coli BMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6HA [auth g]177Escherichia coli BMutation(s): 0 
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Entity ID: 35
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50S ribosomal protein L9IA [auth h]149Escherichia coli BMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13JA [auth i]142Escherichia coli BMutation(s): 0 
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Entity ID: 37
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50S ribosomal protein L14KA [auth j]123Escherichia coli BMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L15LA [auth k]144Escherichia coli BMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16MA [auth l]136Escherichia coli BMutation(s): 1 
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Entity ID: 40
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50S ribosomal protein L17NA [auth m]127Escherichia coli BMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L18OA [auth n]117Escherichia coli BMutation(s): 0 
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50S ribosomal protein L19PA [auth o]115Escherichia coli BMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20QA [auth p]118Escherichia coli BMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21RA [auth q]103Escherichia coli BMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22SA [auth r]110Escherichia coli BMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23TA [auth s]100Escherichia coli BMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24UA [auth t]104Escherichia coli BMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25VA [auth u]94Escherichia coli BMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27WA [auth v]85Escherichia coli BMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28XA [auth w]78Escherichia coli BMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29YA [auth x]63Escherichia coli BMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30ZA [auth y]59Escherichia coli BMutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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UniProt GroupP0AG51
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AB [auth z]57Escherichia coli BMutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7N4
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UniProt GroupP0A7N4
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Entity ID: 5
MoleculeChains LengthOrganismImage
16S rRNAE [auth A]1,554Escherichia coli B
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Entity ID: 26
MoleculeChains LengthOrganismImage
mRNAZ [auth X]6Escherichia coli B
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Entity ID: 27
MoleculeChains LengthOrganismImage
P-site tRNAAA [auth Z]77Escherichia coli B
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Entity ID: 28
MoleculeChains LengthOrganismImage
23S rRNABA [auth a]2,925Escherichia coli B
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Entity ID: 29
MoleculeChains LengthOrganismImage
5S rRNACA [auth b]119Escherichia coli B
Sequence Annotations
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BB [auth 3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AD [auth A]
AG [auth A]
AJ [auth a]
AL [auth a]
AM [auth a]
AD [auth A],
AG [auth A],
AJ [auth a],
AL [auth a],
AM [auth a],
AR [auth a],
AU [auth a],
AV [auth c],
BD [auth A],
BG [auth A],
BJ [auth a],
BL [auth a],
BM [auth a],
BR [auth a],
CB [auth A],
CD [auth A],
CG [auth A],
CJ [auth a],
CL [auth a],
CM [auth a],
CR [auth a],
CV [auth c],
DB [auth A],
DD [auth A],
DG [auth A],
DJ [auth a],
DL [auth a],
DM [auth a],
DQ [auth a],
DR [auth a],
EB [auth A],
ED [auth A],
EG [auth A],
EL [auth a],
EQ [auth a],
ER [auth a],
EV [auth c],
FB [auth A],
FD [auth A],
FG [auth A],
FL [auth a],
FQ [auth a],
FR [auth a],
FV [auth c],
GB [auth A],
GD [auth A],
GG [auth A],
GL [auth a],
GQ [auth a],
GR [auth a],
HD [auth A],
HG [auth A],
HL [auth a],
HQ [auth a],
HR [auth a],
HV [auth d],
ID [auth A],
IG [auth A],
IL [auth a],
IQ [auth a],
IR [auth a],
IV [auth e],
JD [auth A],
JG [auth A],
JK [auth a],
JL [auth a],
JQ [auth a],
JR [auth a],
JV [auth f],
KD [auth A],
KG [auth A],
KK [auth a],
KL [auth a],
KN [auth a],
KQ [auth a],
KR [auth a],
LD [auth A],
LG [auth A],
LK [auth a],
LL [auth a],
LN [auth a],
LQ [auth a],
LR [auth a],
MD [auth A],
MK [auth a],
ML [auth a],
MN [auth a],
MQ [auth a],
MR [auth a],
ND [auth A],
NK [auth a],
NL [auth a],
NN [auth a],
NQ [auth a],
NR [auth a],
OD [auth A],
OK [auth a],
OL [auth a],
ON [auth a],
OQ [auth a],
OR [auth a],
PD [auth A],
PK [auth a],
PL [auth a],
PN [auth a],
PQ [auth a],
PR [auth a],
QD [auth A],
QK [auth a],
QL [auth a],
QN [auth a],
QQ [auth a],
RK [auth a],
RL [auth a],
RQ [auth a],
RT [auth a],
SK [auth a],
SL [auth a],
SQ [auth a],
ST [auth a],
TC [auth A],
TF [auth A],
TK [auth a],
TL [auth a],
TQ [auth a],
TT [auth a],
UC [auth A],
UF [auth A],
UK [auth a],
UL [auth a],
UQ [auth a],
UT [auth a],
VC [auth A],
VF [auth A],
VI [auth a],
VK [auth a],
VL [auth a],
VQ [auth a],
VT [auth a],
WC [auth A],
WF [auth A],
WI [auth a],
WK [auth a],
WL [auth a],
WQ [auth a],
WT [auth a],
XC [auth A],
XF [auth A],
XI [auth a],
XK [auth a],
XL [auth a],
XQ [auth a],
XT [auth a],
YC [auth A],
YF [auth A],
YI [auth a],
YK [auth a],
YL [auth a],
YQ [auth a],
YT [auth a],
ZC [auth A],
ZF [auth A],
ZI [auth a],
ZK [auth a],
ZL [auth a],
ZQ [auth a],
ZT [auth a],
ZU [auth b]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AE [auth A]
AF [auth A]
AH [auth a]
AI [auth a]
AC [auth A],
AE [auth A],
AF [auth A],
AH [auth a],
AI [auth a],
AK [auth a],
AN [auth a],
AO [auth a],
AP [auth a],
AQ [auth a],
AS [auth a],
AT [auth a],
BC [auth A],
BE [auth A],
BF [auth A],
BH [auth a],
BI [auth a],
BK [auth a],
BN [auth a],
BO [auth a],
BP [auth a],
BQ [auth a],
BS [auth a],
BT [auth a],
BU [auth a],
BV [auth c],
CC [auth A],
CE [auth A],
CF [auth A],
CH [auth a],
CI [auth a],
CK [auth a],
CN [auth a],
CO [auth a],
CP [auth a],
CQ [auth a],
CS [auth a],
CT [auth a],
CU [auth a],
DC [auth A],
DE [auth A],
DF [auth A],
DH [auth a],
DI [auth a],
DK [auth a],
DN [auth a],
DO [auth a],
DP [auth a],
DS [auth a],
DT [auth a],
DU [auth a],
DV [auth c],
EC [auth A],
EE [auth A],
EF [auth A],
EH [auth a],
EI [auth a],
EJ [auth a],
EK [auth a],
EM [auth a],
EN [auth a],
EO [auth a],
EP [auth a],
ES [auth a],
ET [auth a],
EU [auth a],
FC [auth A],
FE [auth A],
FF [auth A],
FH [auth a],
FI [auth a],
FJ [auth a],
FK [auth a],
FM [auth a],
FN [auth a],
FO [auth a],
FP [auth a],
FS [auth a],
FT [auth a],
FU [auth a],
GC [auth A],
GE [auth A],
GF [auth A],
GH [auth a],
GI [auth a],
GJ [auth a],
GK [auth a],
GM [auth a],
GN [auth a],
GO [auth a],
GP [auth a],
GS [auth a],
GT [auth a],
GU [auth a],
GV [auth d],
HB [auth A],
HC [auth A],
HE [auth A],
HF [auth A],
HH [auth a],
HI [auth a],
HJ [auth a],
HK [auth a],
HM [auth a],
HN [auth a],
HO [auth a],
HP [auth a],
HS [auth a],
HT [auth a],
HU [auth a],
IB [auth A],
IC [auth A],
IE [auth A],
IF [auth A],
IH [auth a],
II [auth a],
IJ [auth a],
IK [auth a],
IM [auth a],
IN [auth a],
IO [auth a],
IP [auth a],
IS [auth a],
IT [auth a],
IU [auth a],
JB [auth A],
JC [auth A],
JE [auth A],
JF [auth A],
JH [auth a],
JI [auth a],
JJ [auth a],
JM [auth a],
JN [auth a],
JO [auth a],
JP [auth a],
JS [auth a],
JT [auth a],
JU [auth a],
KB [auth A],
KC [auth A],
KE [auth A],
KF [auth A],
KH [auth a],
KI [auth a],
KJ [auth a],
KM [auth a],
KO [auth a],
KP [auth a],
KS [auth a],
KT [auth a],
KU [auth a],
KV [auth z],
LB [auth A],
LC [auth A],
LE [auth A],
LF [auth A],
LH [auth a],
LI [auth a],
LJ [auth a],
LM [auth a],
LO [auth a],
LP [auth a],
LS [auth a],
LT [auth a],
LU [auth a],
MB [auth A],
MC [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth a],
MI [auth a],
MJ [auth a],
MM [auth a],
MO [auth a],
MP [auth a],
MS [auth a],
MT [auth a],
MU [auth a],
NB [auth A],
NC [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth a],
NI [auth a],
NJ [auth a],
NM [auth a],
NO [auth a],
NP [auth a],
NS [auth a],
NT [auth a],
NU [auth a],
OB [auth A],
OC [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth a],
OI [auth a],
OJ [auth a],
OM [auth a],
OO [auth a],
OP [auth a],
OS [auth a],
OT [auth a],
OU [auth a],
PB [auth A],
PC [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth a],
PI [auth a],
PJ [auth a],
PM [auth a],
PO [auth a],
PP [auth a],
PS [auth a],
PT [auth a],
PU [auth a],
QB [auth A],
QC [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth a],
QI [auth a],
QJ [auth a],
QM [auth a],
QO [auth a],
QP [auth a],
QR [auth a],
QS [auth a],
QT [auth a],
QU [auth a],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth X],
RH [auth a],
RI [auth a],
RJ [auth a],
RM [auth a],
RN [auth a],
RO [auth a],
RP [auth a],
RR [auth a],
RS [auth a],
RU [auth a],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
SM [auth a],
SN [auth a],
SO [auth a],
SP [auth a],
SR [auth a],
SS [auth a],
SU [auth a],
TB [auth A],
TD [auth A],
TE [auth A],
TG [auth a],
TH [auth a],
TI [auth a],
TJ [auth a],
TM [auth a],
TN [auth a],
TO [auth a],
TP [auth a],
TR [auth a],
TS [auth a],
TU [auth a],
UB [auth A],
UD [auth A],
UE [auth A],
UG [auth a],
UH [auth a],
UI [auth a],
UJ [auth a],
UM [auth a],
UN [auth a],
UO [auth a],
UP [auth a],
UR [auth a],
US [auth a],
UU [auth b],
VB [auth A],
VD [auth A],
VE [auth A],
VG [auth a],
VH [auth a],
VJ [auth a],
VM [auth a],
VN [auth a],
VO [auth a],
VP [auth a],
VR [auth a],
VS [auth a],
VU [auth b],
WB [auth A],
WD [auth A],
WE [auth A],
WG [auth a],
WH [auth a],
WJ [auth a],
WM [auth a],
WN [auth a],
WO [auth a],
WP [auth a],
WR [auth a],
WS [auth a],
WU [auth b],
XB [auth A],
XD [auth A],
XE [auth A],
XG [auth a],
XH [auth a],
XJ [auth a],
XM [auth a],
XN [auth a],
XO [auth a],
XP [auth a],
XR [auth a],
XS [auth a],
XU [auth b],
YB [auth A],
YD [auth A],
YE [auth A],
YG [auth a],
YH [auth a],
YJ [auth a],
YM [auth a],
YN [auth a],
YO [auth a],
YP [auth a],
YR [auth a],
YS [auth a],
YU [auth b],
ZB [auth A],
ZD [auth A],
ZE [auth A],
ZG [auth a],
ZH [auth a],
ZJ [auth a],
ZM [auth a],
ZN [auth a],
ZO [auth a],
ZP [auth a],
ZR [auth a],
ZS [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
P [auth L]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
EA [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
MA [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--
Other government--
Irish Research CouncilIrelandIRCLA/2019/74
iNEXT-DiscoveryEuropean Union871037

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-03-08
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2024-04-24
    Changes: Data collection