6I7V

Ribosomal protein paralogs bL31 and bL36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


Re-refinement Note

This entry reflects an alternative modeling of the original data in:4YBB


Literature

Bacterial ribosome heterogeneity: Changes in ribosomal protein composition during transition into stationary growth phase.

Lilleorg, S.Reier, K.Pulk, A.Liiv, A.Tammsalu, T.Peil, L.Cate, J.D.Remme, J.

(2018) Biochimie 156: 169-180

  • DOI: 10.1016/j.biochi.2018.10.013
  • Primary Citation of Related Structures:  
    6I7V

  • PubMed Abstract: 
  • Ribosomes consist of many small proteins and few large RNA molecules. Both components are necessary for ribosome functioning during translation. According to widely accepted view, bacterial ribosomes contain always the same complement of ribosomal pr ...

    Ribosomes consist of many small proteins and few large RNA molecules. Both components are necessary for ribosome functioning during translation. According to widely accepted view, bacterial ribosomes contain always the same complement of ribosomal proteins. Comparative bacterial genomics data indicates that several ribosomal proteins are encoded by multiple paralogous genes suggesting structural heterogeneity of ribosomes. In E. coli, two r-proteins bL31 and bL36 are encoded by two genes: rpmE and ykgM encode bL31 protein paralogs bL31A and bL31B, and rpmJ and ykgO encode bL36 protein paralogs bL36A and bL36B respectively. We have found several similarities and differences between ribosomes of exponential and stationary growth phases by using quantitative mass spectrometry and X-ray crystallography. First, composition of ribosome associating proteins changes profoundly as cells transition from exponential to stationary growth phase. Ribosomal core proteins bL31A and bL36A are replaced by bL31B and bL36B, respectively. Second, our X-ray structure of the 70S ribosome demonstrates that bL31B and bL36B proteins have similar ribosome binding sites to their A counterparts. Third, ribosome subpopulations containing A or B paralogs existed simultaneously demonstrating that E. coli ribosomes are heterogeneous with respect to their paralogous ribosomal protein composition that changes via protein exchange.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, University of Tartu, Riia 23B, Tartu, 51010, Estonia. Electronic address: jremme@ut.ee.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2ABBB218Escherichia coliMutation(s): 0 
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Entity ID: 8
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30S ribosomal protein S4ADBD205Escherichia coliMutation(s): 0 
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Entity ID: 9
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30S ribosomal protein S5AEBE150Escherichia coliMutation(s): 0 
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Entity ID: 10
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30S ribosomal protein S6AFBF100Escherichia coliMutation(s): 0 
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Entity ID: 12
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30S ribosomal protein S8AHBH129Escherichia coliMutation(s): 0 
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Entity ID: 14
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30S ribosomal protein S10AJBJ98Escherichia coliMutation(s): 0 
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Entity ID: 15
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30S ribosomal protein S11AKBK117Escherichia coliMutation(s): 0 
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Entity ID: 16
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30S ribosomal protein S12AL123Escherichia coliMutation(s): 0 
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Entity ID: 17
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30S ribosomal protein S13AMBM114Escherichia coliMutation(s): 0 
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Entity ID: 18
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30S ribosomal protein S14ANBN100Escherichia coliMutation(s): 0 
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Entity ID: 21
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30S ribosomal protein S17AQBQ80Escherichia coliMutation(s): 0 
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Entity ID: 22
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30S ribosomal protein S18ARBR55Escherichia coliMutation(s): 0 
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Entity ID: 23
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30S ribosomal protein S19ASBS79Escherichia coliMutation(s): 0 
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Entity ID: 24
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30S ribosomal protein S20ATBT85Escherichia coliMutation(s): 0 
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Entity ID: 25
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30S ribosomal protein S21AUBU54Escherichia coliMutation(s): 0 
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Entity ID: 26
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30S ribosomal protein S12BL123Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L5CFDF177Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L9CHDH148Escherichia coliMutation(s): 0 
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50S ribosomal protein L13CKDK142Escherichia coliMutation(s): 0 
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Entity ID: 36
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50S ribosomal protein L15CMDM144Escherichia coliMutation(s): 0 
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Entity ID: 37
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50S ribosomal protein L16CNDN136Escherichia coliMutation(s): 0 
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50S ribosomal protein L18CPDP117Escherichia coliMutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L19CQDQ114Escherichia coliMutation(s): 0 
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Entity ID: 44
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50S ribosomal protein L23CUDU93Escherichia coliMutation(s): 0 
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Entity ID: 45
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50S ribosomal protein L24CVDV102Escherichia coliMutation(s): 0 
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Entity ID: 46
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50S ribosomal protein L25CWDW94Escherichia coliMutation(s): 0 
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Entity ID: 47
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50S ribosomal protein L27CXDX76Escherichia coliMutation(s): 0 
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Entity ID: 48
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50S ribosomal protein L28CYDY77Escherichia coliMutation(s): 0 
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Entity ID: 49
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50S ribosomal protein L29CZDZ62Escherichia coliMutation(s): 0 
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Entity ID: 50
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50S ribosomal protein L30C0D058Escherichia coliMutation(s): 0 
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Entity ID: 51
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50S ribosomal protein L32C1D156Escherichia coliMutation(s): 0 
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Entity ID: 53
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50S ribosomal protein L34C3D346Escherichia coliMutation(s): 0 
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Entity ID: 56
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50S ribosomal protein L3DD209Escherichia coliMutation(s): 0 
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Entity ID: 57
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50S ribosomal protein L31 type BD768Escherichia coliMutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S7AGBG151Escherichia coliMutation(s): 0 
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Entity ID: 13
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30S ribosomal protein S9AIBI127Escherichia coliMutation(s): 0 
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Entity ID: 19
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30S ribosomal protein S15AOBO88Escherichia coliMutation(s): 0 
Gene Names: 
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30S ribosomal protein S16APBP82Escherichia coliMutation(s): 0 
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50S ribosomal protein L2CCDC271Escherichia coliMutation(s): 0 
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50S ribosomal protein L3CD209Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L4CEDE201Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L6CGDG176Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L11CJDJ141Escherichia coliMutation(s): 0 
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50S ribosomal protein L14CLDL123Escherichia coliMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L17CODO120Escherichia coliMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L20CRDR117Escherichia coliMutation(s): 0 
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Entity ID: 42
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50S ribosomal protein L21CSDS103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22CTDT110Escherichia coliMutation(s): 0 
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Entity ID: 52
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50S ribosomal protein L33C2D251Escherichia coliMutation(s): 0 
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Entity ID: 54
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50S ribosomal protein L35C4D464Escherichia coliMutation(s): 0 
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Entity ID: 55
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50S ribosomal protein L36 2C5D545Escherichia coliMutation(s): 0 
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Entity ID: 7
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30S ribosomal protein S3ACBC206Escherichia coliMutation(s): 0 
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16S ribosmal RNAAA1533Escherichia coli
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23S ribosomal RNADA2903Escherichia coli
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16S ribosomal RNABA1533Escherichia coli
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23S ribsomal RNACA2904Escherichia coli
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5S ribosomal RNACB, DB119Escherichia coli
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

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DA
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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BA, DA, DQ, DR, DS
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GUN
Query on GUN

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DA
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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AA, D3, DA, DD, DS, DT, DU
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

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DA
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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AA, DA, DE, DK, DN, DT
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PEG
Query on PEG

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D1, D3, DA, DP, DQ
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

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D5, DA, DM, DP
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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D1, DA, DB, DR
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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DA
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, BA, C3, CA, CB, CM, CR, D5, DA, DB, DD, DM, DR
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
D2T
Query on D2T
ALL-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
DDL-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.02α = 90
b = 434.57β = 90
c = 623.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States--
Estonia--

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release