6PJ6

High resolution cryo-EM structure of E.coli 50S

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-06-27 Released: 2020-01-22 
  • Deposition Author(s): Stojkovic, V., Myasnikov, A., Frost, A., Fujimori, D.G.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 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

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Stojkovic, V.Myasnikov, A.G.Young, I.D.Frost, A.Fraser, J.S.Fujimori, D.G.

(2020) Nucleic Acids Res 48: 2723-2732

  • DOI: 10.1093/nar/gkaa037
  • Primary Citation of Related Structures:  
    6PJ6

  • PubMed Abstract: 
  • Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis ...

    Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, MC2280 San Francisco, CA 94158, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth K]271Escherichia coliMutation(s): 0 
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Find proteins for A0A1X3I1Y9 (Escherichia coli M056)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth L]209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth M]201Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth N]177Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth O]176Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth P]149Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11I [auth Q]134Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth R]142Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth S]122Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth T]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: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth U]136Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L17N [auth V]120Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L18O [auth W]117Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L19P [auth X]114Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L20Q [auth Y]117Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L21R [auth Z]103Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L22S [auth a]110Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L23T [auth b]93Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L24U [auth c]102Escherichia coliMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L25V [auth d]94Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L27W [auth e]75Escherichia coliMutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L28X [auth f]77Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L29Y [auth g]62Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L30Z [auth h]58Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L32AA [auth i]56Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth j]50Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L34CA [auth k]46Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L35DA [auth l]64Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth m]38Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S rRNAA [auth I]2904Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S rRNAB [auth J]118Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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JH [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth I],
AC [auth I],
AD [auth I],
AE [auth I],
AF [auth I],
AB [auth I],
AC [auth I],
AD [auth I],
AE [auth I],
AF [auth I],
AG [auth I],
AH [auth I],
BB [auth I],
BC [auth I],
BD [auth I],
BE [auth I],
BF [auth I],
BG [auth I],
BH [auth I],
CB [auth I],
CC [auth I],
CD [auth I],
CE [auth I],
CF [auth I],
CG [auth I],
CH [auth I],
DB [auth I],
DC [auth I],
DD [auth I],
DE [auth I],
DF [auth I],
DG [auth I],
DH [auth I],
EB [auth I],
EC [auth I],
ED [auth I],
EE [auth I],
EF [auth I],
EG [auth I],
EH [auth I],
FA [auth I],
FB [auth I],
FC [auth I],
FD [auth I],
FE [auth I],
FF [auth I],
FG [auth I],
FH [auth J],
GA [auth I],
GB [auth I],
GC [auth I],
GD [auth I],
GE [auth I],
GF [auth I],
GG [auth I],
GH [auth K],
HA [auth I],
HB [auth I],
HC [auth I],
HD [auth I],
HE [auth I],
HF [auth I],
HG [auth I],
IA [auth I],
IB [auth I],
IC [auth I],
ID [auth I],
IE [auth I],
IF [auth I],
IG [auth I],
IH [auth L],
JA [auth I],
JB [auth I],
JC [auth I],
JD [auth I],
JE [auth I],
JF [auth I],
JG [auth I],
KA [auth I],
KB [auth I],
KC [auth I],
KD [auth I],
KE [auth I],
KF [auth I],
KG [auth I],
LA [auth I],
LB [auth I],
LC [auth I],
LD [auth I],
LE [auth I],
LF [auth I],
LG [auth I],
MA [auth I],
MB [auth I],
MC [auth I],
MD [auth I],
ME [auth I],
MF [auth I],
MG [auth I],
NA [auth I],
NB [auth I],
NC [auth I],
ND [auth I],
NE [auth I],
NF [auth I],
NG [auth I],
OA [auth I],
OB [auth I],
OC [auth I],
OD [auth I],
OE [auth I],
OF [auth I],
OG [auth I],
PA [auth I],
PB [auth I],
PC [auth I],
PD [auth I],
PE [auth I],
PF [auth I],
PG [auth I],
QA [auth I],
QB [auth I],
QC [auth I],
QD [auth I],
QE [auth I],
QF [auth I],
QG [auth I],
RA [auth I],
RB [auth I],
RC [auth I],
RD [auth I],
RE [auth I],
RF [auth I],
RG [auth I],
SA [auth I],
SB [auth I],
SC [auth I],
SD [auth I],
SE [auth I],
SF [auth I],
SG [auth I],
TA [auth I],
TB [auth I],
TC [auth I],
TD [auth I],
TE [auth I],
TF [auth I],
TG [auth I],
UA [auth I],
UB [auth I],
UC [auth I],
UD [auth I],
UE [auth I],
UF [auth I],
UG [auth I],
VA [auth I],
VB [auth I],
VC [auth I],
VD [auth I],
VE [auth I],
VF [auth I],
VG [auth I],
WA [auth I],
WB [auth I],
WC [auth I],
WD [auth I],
WE [auth I],
WF [auth I],
WG [auth I],
XA [auth I],
XB [auth I],
XC [auth I],
XD [auth I],
XE [auth I],
XF [auth I],
XG [auth I],
YA [auth I],
YB [auth I],
YC [auth I],
YD [auth I],
YE [auth I],
YF [auth I],
YG [auth I],
ZA [auth I],
ZB [auth I],
ZC [auth I],
ZD [auth I],
ZE [auth I],
ZF [auth I],
ZG [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
HH [auth K]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4D4
Query on 4D4
M [auth U]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 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 Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI137270
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1R01GM127673-01
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States5P50GM082545-12

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references