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


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 proteins ...

    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.



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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth AB], AA [auth BB]218Escherichia coliMutation(s): 0 
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Entity ID: 7
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30S ribosomal protein S3H [auth AC], BA [auth BC]206Escherichia coliMutation(s): 0 
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Entity ID: 8
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30S ribosomal protein S4I [auth AD], CA [auth BD]205Escherichia coliMutation(s): 0 
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Entity ID: 9
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30S ribosomal protein S5J [auth AE], DA [auth BE]150Escherichia coliMutation(s): 0 
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Entity ID: 10
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30S ribosomal protein S6K [auth AF], EA [auth BF]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7L [auth AG], FA [auth BG]151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8M [auth AH], GA [auth BH]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9N [auth AI], HA [auth BI]127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10O [auth AJ], IA [auth BJ]98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11P [auth AK], JA [auth BK]117Escherichia coliMutation(s): 0 
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Entity ID: 16
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30S ribosomal protein S12Q [auth AL]123Escherichia coliMutation(s): 0 
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30S ribosomal protein S13R [auth AM], LA [auth BM]114Escherichia coliMutation(s): 0 
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30S ribosomal protein S14S [auth AN], MA [auth BN]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S15T [auth AO], NA [auth BO]88Escherichia coliMutation(s): 0 
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30S ribosomal protein S16U [auth AP], OA [auth BP]82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17V [auth AQ], PA [auth BQ]80Escherichia coliMutation(s): 0 
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30S ribosomal protein S18W [auth AR], QA [auth BR]55Escherichia coliMutation(s): 0 
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30S ribosomal protein S19X [auth AS], RA [auth BS]79Escherichia coliMutation(s): 0 
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30S ribosomal protein S20Y [auth AT], SA [auth BT]85Escherichia coliMutation(s): 0 
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30S ribosomal protein S21Z [auth AU], TA [auth BU]54Escherichia coliMutation(s): 0 
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30S ribosomal protein S12KA [auth BL]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L2UA [auth CC], XB [auth DC]271Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L3VA [auth CD]209Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L4WA [auth CE], ZB [auth DE]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5XA [auth CF], AC [auth DF]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L6YA [auth CG], BC [auth DG]176Escherichia coliMutation(s): 0 
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50S ribosomal protein L9ZA [auth CH], CC [auth DH]148Escherichia coliMutation(s): 0 
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50S ribosomal protein L11AB [auth CJ], DC [auth DJ]141Escherichia coliMutation(s): 0 
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50S ribosomal protein L13BB [auth CK], EC [auth DK]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14CB [auth CL], FC [auth DL]123Escherichia coliMutation(s): 0 
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Entity ID: 36
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50S ribosomal protein L15DB [auth CM], GC [auth DM]144Escherichia coliMutation(s): 0 
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Entity ID: 37
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50S ribosomal protein L16EB [auth CN], HC [auth DN]136Escherichia coliMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L17FB [auth CO], IC [auth DO]120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18GB [auth CP], JC [auth DP]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19HB [auth CQ], KC [auth DQ]114Escherichia coliMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L20IB [auth CR], LC [auth DR]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L21JB [auth CS], MC [auth DS]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22KB [auth CT], NC [auth DT]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23LB [auth CU], OC [auth DU]93Escherichia coliMutation(s): 0 
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50S ribosomal protein L24MB [auth CV], PC [auth DV]102Escherichia coliMutation(s): 0 
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50S ribosomal protein L25NB [auth CW], QC [auth DW]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27OB [auth CX], RC [auth DX]76Escherichia coliMutation(s): 0 
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Entity ID: 48
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50S ribosomal protein L28PB [auth CY], SC [auth DY]77Escherichia coliMutation(s): 0 
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50S ribosomal protein L29QB [auth CZ], TC [auth DZ]62Escherichia coliMutation(s): 0 
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Entity ID: 50
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50S ribosomal protein L30RB [auth C0], UC [auth D0]58Escherichia coliMutation(s): 0 
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50S ribosomal protein L32SB [auth C1], VC [auth D1]56Escherichia coliMutation(s): 0 
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Entity ID: 52
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50S ribosomal protein L33TB [auth C2], WC [auth D2]51Escherichia coliMutation(s): 0 
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Entity ID: 53
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50S ribosomal protein L34UB [auth C3], XC [auth D3]46Escherichia coliMutation(s): 0 
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Entity ID: 54
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50S ribosomal protein L35VB [auth C4], YC [auth D4]64Escherichia coliMutation(s): 0 
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Entity ID: 55
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50S ribosomal protein L36 2WB [auth C5], ZC [auth D5]45Escherichia coliMutation(s): 0 
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Entity ID: 56
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50S ribosomal protein L3YB [auth DD]209Escherichia coliMutation(s): 0 
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Entity ID: 57
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50S ribosomal protein L31 type BAD [auth D7]68Escherichia coliMutation(s): 0 
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Entity ID: 1
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16S ribosomal RNAA [auth AA]1533Escherichia coli
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Entity ID: 2
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16S ribosomal RNAB [auth BA]1533Escherichia coli
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Entity ID: 3
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23S ribosomal RNAC [auth DA]2903Escherichia coli
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Entity ID: 4
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23S ribsomal RNAD [auth CA]2904Escherichia coli
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Entity ID: 5
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5S ribosomal RNAF [auth CB], E [auth DB]119Escherichia coli
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Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

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NI [auth DA], SJ [auth DA]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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BJ [auth DA], HW [auth DQ], JW [auth DR], NW [auth DS], OF [auth BA]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GUN (Subject of Investigation/LOI)
Query on GUN

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FK [auth DA]GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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MW [auth DS], ND [auth AA], OI [auth DA], PW [auth DT], QW [auth DU], TJ [auth DA], TW [auth D3], WV [auth DD]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

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KI [auth DA], PI [auth DA], XJ [auth DA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AW [auth DK] , DW [auth DN] , EK [auth DA] , OW [auth DT] , PD [auth AA] , UJ [auth DA] , WI [auth DA] , YI [auth DA] , 
AW [auth DK],  DW [auth DN],  EK [auth DA],  OW [auth DT],  PD [auth AA],  UJ [auth DA],  WI [auth DA],  YI [auth DA],  YJ [auth DA],  YV [auth DE],  ZI [auth DA],  ZJ [auth DA],  ZV [auth DE]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AK [auth DA] , DJ [auth DA] , EW [auth DP] , GW [auth DQ] , OJ [auth DA] , PJ [auth DA] , QJ [auth DA] , SW [auth D1] , 
AK [auth DA],  DJ [auth DA],  EW [auth DP],  GW [auth DQ],  OJ [auth DA],  PJ [auth DA],  QJ [auth DA],  SW [auth D1],  UW [auth D3]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

Download Ideal Coordinates CCD File 
BW [auth DM], FW [auth DP], HJ [auth DA], LI [auth DA], QI [auth DA], VW [auth D5], WJ [auth DA]1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CK [auth DA] , DK [auth DA] , FJ [auth DA] , JV [auth DB] , KJ [auth DA] , KV [auth DB] , LJ [auth DA] , LV [auth DB] , 
CK [auth DA],  DK [auth DA],  FJ [auth DA],  JV [auth DB],  KJ [auth DA],  KV [auth DB],  LJ [auth DA],  LV [auth DB],  LW [auth DR],  MJ [auth DA],  NJ [auth DA],  RW [auth D1]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
IJ [auth DA], RJ [auth DA], XI [auth DA]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA] , AF [auth AA] , AG [auth BA] , AH [auth BA] , AI [auth DA] , AJ [auth DA] , AL [auth DA] , AM [auth DA] , 
AE [auth AA],  AF [auth AA],  AG [auth BA],  AH [auth BA],  AI [auth DA],  AJ [auth DA],  AL [auth DA],  AM [auth DA],  AN [auth DA],  AO [auth DA],  AP [auth CA],  AQ [auth CA],  AR [auth CA],  AS [auth CA],  AT [auth CA],  AU [auth CA],  AV [auth CA],  BD [auth AA],  BE [auth AA],  BF [auth AA],  BG [auth BA],  BH [auth BA],  BI [auth DA],  BK [auth DA],  BL [auth DA],  BM [auth DA],  BN [auth DA],  BO [auth DA],  BP [auth CA],  BQ [auth CA],  BR [auth CA],  BS [auth CA],  BT [auth CA],  BU [auth CA],  BV [auth CA],  CD [auth AA],  CE [auth AA],  CF [auth AA],  CG [auth BA],  CH [auth BA],  CI [auth DA],  CJ [auth DA],  CL [auth DA],  CM [auth DA],  CN [auth DA],  CO [auth DA],  CP [auth CA],  CQ [auth CA],  CR [auth CA],  CS [auth CA],  CT [auth CA],  CU [auth CA],  CV [auth CA],  CW [auth DM],  DD [auth AA],  DE [auth AA],  DF [auth AA],  DG [auth BA],  DH [auth BA],  DI [auth DA],  DL [auth DA],  DM [auth DA],  DN [auth DA],  DO [auth DA],  DP [auth CA],  DQ [auth CA],  DR [auth CA],  DS [auth CA],  DT [auth CA],  DU [auth CA],  DV [auth CA],  ED [auth AA],  EE [auth AA],  EF [auth AA],  EG [auth BA],  EH [auth BA],  EI [auth DA],  EJ [auth DA],  EL [auth DA],  EM [auth DA],  EN [auth DA],  EO [auth DA],  EP [auth CA],  EQ [auth CA],  ER [auth CA],  ES [auth CA],  ET [auth CA],  EU [auth CA],  EV [auth CA],  FD [auth AA],  FE [auth AA],  FF [auth AA],  FG [auth BA],  FH [auth BA],  FI [auth DA],  FL [auth DA],  FM [auth DA],  FN [auth DA],  FO [auth DA],  FP [auth CA],  FQ [auth CA],  FR [auth CA],  FS [auth CA],  FT [auth CA],  FU [auth CA],  FV [auth CA],  GD [auth AA],  GE [auth AA],  GF [auth AA],  GG [auth BA],  GH [auth DA],  GI [auth DA],  GJ [auth DA],  GK [auth DA],  GL [auth DA],  GM [auth DA],  GN [auth DA],  GO [auth DA],  GP [auth CA],  GQ [auth CA],  GR [auth CA],  GS [auth CA],  GT [auth CA],  GU [auth CA],  GV [auth CA],  HD [auth AA],  HE [auth AA],  HF [auth AA],  HG [auth BA],  HH [auth DA],  HI [auth DA],  HK [auth DA],  HL [auth DA],  HM [auth DA],  HN [auth DA],  HO [auth DA],  HP [auth CA],  HQ [auth CA],  HR [auth CA],  HS [auth CA],  HT [auth CA],  HU [auth CA],  HV [auth CA],  ID [auth AA],  IE [auth AA],  IF [auth BA],  IG [auth BA],  IH [auth DA],  II [auth DA],  IK [auth DA],  IL [auth DA],  IM [auth DA],  IN [auth DA],  IO [auth DA],  IP [auth CA],  IQ [auth CA],  IR [auth CA],  IS [auth CA],  IT [auth CA],  IU [auth CA],  IV [auth CA],  IW [auth DR],  JD [auth AA],  JE [auth AA],  JF [auth BA],  JG [auth BA],  JH [auth DA],  JI [auth DA],  JJ [auth DA],  JK [auth DA],  JL [auth DA],  JM [auth DA],  JN [auth DA],  JO [auth DA],  JP [auth CA],  JQ [auth CA],  JR [auth CA],  JS [auth CA],  JT [auth CA],  JU [auth CA],  KD [auth AA],  KE [auth AA],  KF [auth BA],  KG [auth BA],  KH [auth DA],  KK [auth DA],  KL [auth DA],  KM [auth DA],  KN [auth DA],  KO [auth DA],  KP [auth CA],  KQ [auth CA],  KR [auth CA],  KS [auth CA],  KT [auth CA],  KU [auth CA],  KW [auth DR],  LD [auth AA],  LE [auth AA],  LF [auth BA],  LG [auth BA],  LH [auth DA],  LK [auth DA],  LL [auth DA],  LM [auth DA],  LN [auth DA],  LO [auth DA],  LP [auth CA],  LQ [auth CA],  LR [auth CA],  LS [auth CA],  LT [auth CA],  LU [auth CA],  MD [auth AA],  ME [auth AA],  MF [auth BA],  MG [auth BA],  MH [auth DA],  MI [auth DA],  MK [auth DA],  ML [auth DA],  MM [auth DA],  MN [auth DA],  MO [auth DA],  MP [auth CA],  MQ [auth CA],  MR [auth CA],  MS [auth CA],  MT [auth CA],  MU [auth CA],  MV [auth DB],  NE [auth AA],  NF [auth BA],  NG [auth BA],  NH [auth DA],  NK [auth DA],  NL [auth DA],  NM [auth DA],  NN [auth DA],  NO [auth DA],  NP [auth CA],  NQ [auth CA],  NR [auth CA],  NS [auth CA],  NT [auth CA],  NU [auth CA],  NV [auth DB],  OD [auth AA],  OE [auth AA],  OG [auth BA],  OH [auth DA],  OK [auth DA],  OL [auth DA],  OM [auth DA],  ON [auth DA],  OO [auth DA],  OP [auth CA],  OQ [auth CA],  OR [auth CA],  OS [auth CA],  OT [auth CA],  OU [auth CA],  OV [auth DB],  PE [auth AA],  PF [auth BA],  PG [auth BA],  PH [auth DA],  PK [auth DA],  PL [auth DA],  PM [auth DA],  PN [auth DA],  PO [auth CA],  PP [auth CA],  PQ [auth CA],  PR [auth CA],  PS [auth CA],  PT [auth CA],  PU [auth CA],  PV [auth DB],  QD [auth AA],  QE [auth AA],  QF [auth BA],  QG [auth BA],  QH [auth DA],  QK [auth DA],  QL [auth DA],  QM [auth DA],  QN [auth DA],  QO [auth CA],  QP [auth CA],  QQ [auth CA],  QR [auth CA],  QS [auth CA],  QT [auth CA],  QU [auth CA],  QV [auth CB],  RD [auth AA],  RE [auth AA],  RF [auth BA],  RG [auth BA],  RH [auth DA],  RI [auth DA],  RK [auth DA],  RL [auth DA],  RM [auth DA],  RN [auth DA],  RO [auth CA],  RP [auth CA],  RQ [auth CA],  RR [auth CA],  RS [auth CA],  RT [auth CA],  RU [auth CA],  RV [auth CB],  SD [auth AA],  SE [auth AA],  SF [auth BA],  SG [auth BA],  SH [auth DA],  SI [auth DA],  SK [auth DA],  SL [auth DA],  SM [auth DA],  SN [auth DA],  SO [auth CA],  SP [auth CA],  SQ [auth CA],  SR [auth CA],  SS [auth CA],  ST [auth CA],  SU [auth CA],  SV [auth CB],  TD [auth AA],  TE [auth AA],  TF [auth BA],  TG [auth BA],  TH [auth DA],  TI [auth DA],  TK [auth DA],  TL [auth DA],  TM [auth DA],  TN [auth DA],  TO [auth CA],  TP [auth CA],  TQ [auth CA],  TR [auth CA],  TS [auth CA],  TT [auth CA],  TU [auth CA],  TV [auth CM],  UD [auth AA],  UE [auth AA],  UF [auth BA],  UG [auth BA],  UH [auth DA],  UI [auth DA],  UK [auth DA],  UL [auth DA],  UM [auth DA],  UN [auth DA],  UO [auth CA],  UP [auth CA],  UQ [auth CA],  UR [auth CA],  US [auth CA],  UT [auth CA],  UU [auth CA],  UV [auth CR],  VD [auth AA],  VE [auth AA],  VF [auth BA],  VG [auth BA],  VH [auth DA],  VI [auth DA],  VJ [auth DA],  VK [auth DA],  VL [auth DA],  VM [auth DA],  VN [auth DA],  VO [auth CA],  VP [auth CA],  VQ [auth CA],  VR [auth CA],  VS [auth CA],  VT [auth CA],  VU [auth CA],  VV [auth C3],  WD [auth AA],  WE [auth AA],  WF [auth BA],  WG [auth BA],  WH [auth DA],  WK [auth DA],  WL [auth DA],  WM [auth DA],  WN [auth DA],  WO [auth CA],  WP [auth CA],  WQ [auth CA],  WR [auth CA],  WS [auth CA],  WT [auth CA],  WU [auth CA],  WW [auth D5],  XD [auth AA],  XE [auth AA],  XF [auth BA],  XG [auth BA],  XH [auth DA],  XK [auth DA],  XL [auth DA],  XM [auth DA],  XN [auth DA],  XO [auth CA],  XP [auth CA],  XQ [auth CA],  XR [auth CA],  XS [auth CA],  XT [auth CA],  XU [auth CA],  XV [auth DD],  YD [auth AA],  YE [auth AA],  YF [auth BA],  YG [auth BA],  YH [auth DA],  YK [auth DA],  YL [auth DA],  YM [auth DA],  YN [auth DA],  YO [auth CA],  YP [auth CA],  YQ [auth CA],  YR [auth CA],  YS [auth CA],  YT [auth CA],  YU [auth CA],  ZD [auth AA],  ZE [auth AA],  ZF [auth BA],  ZG [auth BA],  ZH [auth DA],  ZK [auth DA],  ZL [auth DA],  ZM [auth DA],  ZN [auth DA],  ZO [auth CA],  ZP [auth CA],  ZQ [auth CA],  ZR [auth CA],  ZS [auth CA],  ZT [auth CA],  ZU [auth CA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
D2T
Query on D2T
Q [auth AL]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
YB [auth DD]L-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



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States--
Estonia--

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Data collection, Database references, Derived calculations, Structure summary