6PJ6

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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. --: --

  • DOI: 10.1093/nar/gkaa037

  • 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 an ...

    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 Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, MC2280 San Francisco, CA 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
K
271Escherichia coli M056Mutation(s): 0 
Gene Names: rplB
Find proteins for A0A1X3I1Y9 (Escherichia coli M056)
Go to UniProtKB:  A0A1X3I1Y9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
L
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
M
201Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplD
Find proteins for D7Z9F6 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9F6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
N
177Escherichia coli DEC2CMutation(s): 0 
Gene Names: rplE
Find proteins for H4KMS0 (Escherichia coli DEC2C)
Go to UniProtKB:  H4KMS0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
O
176Escherichia coli 1-392-07_S4_C3Mutation(s): 0 
Gene Names: rplF
Find proteins for A0A080FKA9 (Escherichia coli 1-392-07_S4_C3)
Go to UniProtKB:  A0A080FKA9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
P
149Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplI
Find proteins for D7ZI15 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZI15
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
Q
134N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
R
142Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplM
Find proteins for D7ZET0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZET0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
S
122Escherichia coli MS 115-1Mutation(s): 0 
Gene Names: rplN
Find proteins for D7Y3D0 (Escherichia coli MS 115-1)
Go to UniProtKB:  D7Y3D0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
T
144Escherichia coliMutation(s): 0 
Gene Names: rplO
Find proteins for A0A037Y8L6 (Escherichia coli)
Go to UniProtKB:  A0A037Y8L6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
U
136Escherichia coli B185Mutation(s): 0 
Gene Names: rplP
Find proteins for D6IEL1 (Escherichia coli B185)
Go to UniProtKB:  D6IEL1
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
V
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
W
117Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplR
Find proteins for D7Z9H1 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9H1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
X
114Escherichia coli KTE10Mutation(s): 0 
Gene Names: rplS
Find proteins for L2UTN8 (Escherichia coli KTE10)
Go to UniProtKB:  L2UTN8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Y
117Escherichia coli ISC56Mutation(s): 0 
Gene Names: rplT
Find proteins for W1HFV2 (Escherichia coli ISC56)
Go to UniProtKB:  W1HFV2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
Z
103Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplU
Find proteins for D7ZEN7 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7ZEN7
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
a
110Escherichia coli MS 69-1Mutation(s): 0 
Gene Names: rplV
Find proteins for D7Z9G0 (Escherichia coli MS 69-1)
Go to UniProtKB:  D7Z9G0
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
b
93Escherichia coli chi7122Mutation(s): 0 
Gene Names: rplW
Find proteins for J7RVN9 (Escherichia coli chi7122)
Go to UniProtKB:  J7RVN9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
c
102Escherichia coli 113303Mutation(s): 0 
Gene Names: rplX
Find proteins for U9Y1I5 (Escherichia coli 113303)
Go to UniProtKB:  U9Y1I5
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
d
94Escherichia coli MS 84-1Mutation(s): 0 
Gene Names: rplY
Find proteins for D7XH79 (Escherichia coli MS 84-1)
Go to UniProtKB:  D7XH79
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
e
75Escherichia coli 1-392-07_S4_C1Mutation(s): 0 
Gene Names: rpmA
Find proteins for A0A074HTA6 (Escherichia coli 1-392-07_S4_C1)
Go to UniProtKB:  A0A074HTA6
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
f
77Escherichia coli UMEA 3200-1Mutation(s): 0 
Gene Names: rpmB
Find proteins for T9AVR0 (Escherichia coli UMEA 3200-1)
Go to UniProtKB:  T9AVR0
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
g
62Escherichia coli MS 119-7Mutation(s): 0 
Gene Names: rpmC
Find proteins for D8E8E5 (Escherichia coli MS 119-7)
Go to UniProtKB:  D8E8E5
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
h
58Escherichia coli KTE10Mutation(s): 0 
Gene Names: rpmD
Find proteins for L2VFR0 (Escherichia coli KTE10)
Go to UniProtKB:  L2VFR0
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
i
56Escherichia coli 908573Mutation(s): 0 
Gene Names: rpmF
Find proteins for V0ZMP5 (Escherichia coli 908573)
Go to UniProtKB:  V0ZMP5
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
j
50Escherichia coli TA054Mutation(s): 0 
Gene Names: rpmG
Find proteins for A0A1X3LDF5 (Escherichia coli TA054)
Go to UniProtKB:  A0A1X3LDF5
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
k
46Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: rpmH
Find proteins for B7MGC4 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MGC4
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
l
64Escherichia coli KTE112Mutation(s): 0 
Gene Names: rpmI
Find proteins for L4VIS3 (Escherichia coli KTE112)
Go to UniProtKB:  L4VIS3
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
m
38Escherichia coli (strain UMEA 3162-1)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
Go to UniProtKB:  A0A0E2L017
Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNAI2904Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNAJ118Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
m
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
K
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
I, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  14 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
I
RNA LINKINGC9 H13 N2 O9 PU
4D4
Query on 4D4
U
L-peptide linkingC6 H14 N4 O3ARG
5MC
Query on 5MC
I
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
I
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
I
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
I
RNA LINKINGC11 H16 N5 O8 PG
OMC
Query on OMC
I
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
I
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
I
RNA LINKINGC11 H17 N5 O8 PG
OMG
Query on OMG
I
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
I
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
I
RNA LINKINGC11 H16 N5 O7 PA
3TD
Query on 3TD
I
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
I
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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