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 re ...

    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 L2 K271Escherichia coliMutation(s): 0 
Find proteins for A0A1X3I1Y9 (Escherichia coli M056)
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Entity ID: 4
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50S ribosomal protein L3 L209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
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50S ribosomal protein L4 M201Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 N177Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 O176Escherichia coliMutation(s): 0 
Find proteins for A0A080FKA9 (Escherichia coli 1-392-07_S4_C3)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 P149Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11 Q134Escherichia coliMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L13 R142Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L14 S122Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L15 T144Escherichia coliMutation(s): 0 
Gene Names: 
rplO, A8C65_19395, A9R57_24660, ACU57_21045, AM464_09135, AUQ13_22145, BANRA_01932, BANRA_03684, BHS87_18545, BJJ90_02210, BMA87_18510, BON75_18850, BON98_13310, BUE81_25610, BvCms2454_01416, BvCmsHHP001_00334, BvCmsHHP019_04131, BvCmsHHP056_02703, BvCmsKSP026_02554, BvCmsSINP011_02480, BW690_10710, BZL31_22885, C5F72_02595, C5F73_02860, C5N07_23575, C9E25_20065, C9Z39_20710, CA593_09735, CG692_20270, CI693_13520, CI694_01990, CIG45_22410, D0X26_24495, D2185_22985, D3821_17755, D3O91_20305, D3Y67_24390, D4638_19455, D4718_17880, D9C99_17930, D9D20_21995, D9D44_22490, D9G29_15635, D9G69_20945, D9H68_17710, D9J52_19090, D9Z28_15390, DAH37_14685, DBQ99_03415, DJ503_19770, DL326_22310, DNC98_19095, DT034_22410, DTL43_21000, E2119_19640, E2134_21880, E2135_06185, E4A44_21305, E4K51_21490, E4K55_21420, E4K60_18985, E4K61_20025, E5P22_10480, E5P28_20875, EA213_19860, EAI42_04990, EAI52_16365, EC1094V2_354, EC3234A_55c00230, EC3426_04459, ECTO6_00449, ED307_17010, EEP23_17135, EG808_17075, EI021_21030, EI028_20740, EI032_18995, EI041_20035, EIZ93_12470, EL75_0396, EL79_0415, EL80_0407, ELT20_19170, EPT01_19765, ERS085365_03907, ERS085416_03881, ERS139211_03685, ERS150873_04051, EXX71_21335, EYD11_02080, F1E19_19655, F9040_18095, FRV13_20015, FV293_22465, FWK02_06270, G5632_17770, G5688_20025, GHR40_07050, GKF39_20550, GKF74_18130, GKF86_20070, GKF89_18470, GP671_20580, GP689_20785, GP954_00945, GP979_02005, GQE33_22230, GQE34_14255, GQE64_20420, GQM17_19915, GRW05_09060, GRW27_21285, GRW42_19350, GRW57_03540, GRW80_20585, GRW81_21150, NCTC10963_00456, NCTC11022_03475, NCTC11126_02772, NCTC12650_00710, NCTC13216_01351, NCTC9045_00567, NCTC9062_02686, NCTC9117_00757, NCTC9706_02738, PGD_00585, RK56_021420, SAMEA3472047_03862, SAMEA3472080_04748, SAMEA3484427_04887, SAMEA3484429_04875, SAMEA3752559_00346, SAMEA3753300_02227

Find proteins for A0A037Y8L6 (Escherichia coli)
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Entity ID: 13
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50S ribosomal protein L16 U136Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L17 V120Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L18 W117Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L19 X114Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L20 Y117Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L21 Z103Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L22 a110Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L23 b93Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L24 c102Escherichia coliMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L25 d94Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L27 e75Escherichia coliMutation(s): 0 
Find proteins for A0A074HTA6 (Escherichia coli 1-392-07_S4_C1)
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Entity ID: 24
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50S ribosomal protein L28 f77Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L29 g62Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L30 h58Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L32 i56Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 j50Escherichia coliMutation(s): 0 
Find proteins for A0A1X3LDF5 (Escherichia coli TA054)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 k46Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L35 l64Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L36 m38Escherichia coliMutation(s): 0 
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S rRNAI2904Escherichia coli
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S rRNAJ118Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
m
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
I, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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K
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4D4
Query on 4D4		UL-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 

  • 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