3CMA

The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.

Simonovic, M.Steitz, T.A.

(2008) RNA 14: 2372-2378

  • DOI: 10.1261/rna.1118908
  • Primary Citation of Related Structures:  
    3CME, 3CMA

  • PubMed Abstract: 
  • The last step in ribosome-catalyzed protein synthesis is the hydrolytic release of the newly formed polypeptide from the P-site bound tRNA. Hydrolysis of the ester link of the peptidyl-tRNA is stimulated normally by the binding of release factors (RFs). However, an unacylated tRNA or just CCA binding to the ribosomal A site can also stimulate deacylation under some nonphysiological conditions ...

    The last step in ribosome-catalyzed protein synthesis is the hydrolytic release of the newly formed polypeptide from the P-site bound tRNA. Hydrolysis of the ester link of the peptidyl-tRNA is stimulated normally by the binding of release factors (RFs). However, an unacylated tRNA or just CCA binding to the ribosomal A site can also stimulate deacylation under some nonphysiological conditions. Although the sequence of events is well described by biochemical studies, the structural basis of the mechanism underlying this process is not well understood. Two new structures of the large ribosomal subunit of Haloarcula marismortui complexed with a peptidyl-tRNA analog in the P site and two oligonucleotide mimics of unacylated tRNA, CCA and CA, in the A site show that the binding of either CA or CCA induces a very similar conformational change in the peptidyl-transferase center as induced by aminoacyl-CCA. However, only CCA positions a water molecule appropriately to attack the carbonyl carbon of the peptidyl-tRNA and stabilizes the proper orientation of the ester link for hydrolysis. We, thus, conclude that both the ability of the O3'-hydroxyl group of the A-site A76 to position the water and the A-site CCA induced conformational change of the PTC are critical for the catalysis of the deacylation of the peptidyl-tRNA by CCA, and perhaps, an analogous mechanism is used by RFs.


    Organizational Affiliation

    Howard Hughes Medical Institute, New Haven, Connecticut 06520-8114, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2PA240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3PB338Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4PC246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5PD177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6PE178Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeF120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10EG348Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10eH177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11PI162Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13PJ145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14PK132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15PL165Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15eM196Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18PN187Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18eO116Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19eP149Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21eQ96Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22PR155Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PS85Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24PT120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24eU67Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29PV71Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PW154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31eX92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32eY240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37AeZ116Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37eAA [auth 1]57Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39eBA [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44ECA [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNADA [auth 0]2923Haloarcula marismortui
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Entity ID: 31
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAEA [auth 9]122Haloarcula marismortui
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  • Entity ID: 32
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*CP*CP*A)-3')FA [auth 5]3N/A
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    • Entity ID: 33
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*CP*CP*(8AN))-3')GA [auth 6]3N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 8 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PHE (Subject of Investigation/LOI)
      Query on PHE

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      ZL [auth 6]PHENYLALANINE
      C9 H11 N O2
      COLNVLDHVKWLRT-QMMMGPOBSA-N
       Ligand Interaction
      ACA
      Query on ACA

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      AM [auth 6]6-AMINOHEXANOIC ACID
      C6 H13 N O2
      SLXKOJJOQWFEFD-UHFFFAOYSA-N
       Ligand Interaction
      CD
      Query on CD

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      BC [auth Z], CC [auth 1], IC [auth 3], KB [auth O], XB [auth U]CADMIUM ION
      Cd
      WLZRMCYVCSSEQC-UHFFFAOYSA-N
       Ligand Interaction
      SR
      Query on SR

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      AJ [auth 0] , AK [auth 0] , AL [auth 0] , BJ [auth 0] , BK [auth 0] , BL [auth 0] , CJ [auth 0] , CK [auth 0] , 
      AJ [auth 0],  AK [auth 0],  AL [auth 0],  BJ [auth 0],  BK [auth 0],  BL [auth 0],  CJ [auth 0],  CK [auth 0],  CL [auth 0],  DC [auth 1],  DJ [auth 0],  DK [auth 0],  DL [auth 0],  EC [auth 1],  EJ [auth 0],  EK [auth 0],  EL [auth 0],  FJ [auth 0],  FK [auth 0],  FL [auth 0],  GJ [auth 0],  GK [auth 0],  GL [auth 0],  HC [auth 3],  HJ [auth 0],  HK [auth 0],  HL [auth 0],  IJ [auth 0],  IK [auth 0],  IL [auth 0],  JJ [auth 0],  JK [auth 0],  JL [auth 0],  KA [auth A],  KC [auth 3],  KJ [auth 0],  KK [auth 0],  KL [auth 0],  LA [auth A],  LC [auth 3],  LJ [auth 0],  LK [auth 0],  LL [auth 0],  MA [auth A],  MI [auth 0],  MJ [auth 0],  MK [auth 0],  ML [auth 0],  NI [auth 0],  NJ [auth 0],  NK [auth 0],  NL [auth 0],  OI [auth 0],  OJ [auth 0],  OK [auth 0],  OL [auth 0],  PI [auth 0],  PJ [auth 0],  PK [auth 0],  PL [auth 0],  QA [auth B],  QI [auth 0],  QJ [auth 0],  QK [auth 0],  QL [auth 0],  RA [auth B],  RB [auth R],  RI [auth 0],  RJ [auth 0],  RK [auth 0],  RL [auth 0],  SB [auth S],  SI [auth 0],  SJ [auth 0],  SK [auth 0],  SL [auth 0],  TI [auth 0],  TJ [auth 0],  TK [auth 0],  TL [auth 0],  UB [auth T],  UI [auth 0],  UJ [auth 0],  UK [auth 0],  VA [auth F],  VI [auth 0],  VJ [auth 0],  VK [auth 0],  WA [auth H],  WB [auth T],  WI [auth 0],  WJ [auth 0],  WK [auth 0],  WL [auth 9],  XA [auth H],  XI [auth 0],  XJ [auth 0],  XK [auth 0],  XL [auth 9],  YB [auth Y],  YI [auth 0],  YJ [auth 0],  YK [auth 0],  YL [auth 9],  ZI [auth 0],  ZJ [auth 0],  ZK [auth 0]
      STRONTIUM ION
      Sr
      PWYYWQHXAPXYMF-UHFFFAOYSA-N
       Ligand Interaction
      K
      Query on K

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      SF [auth 0], TF [auth 0]POTASSIUM ION
      K
      NPYPAHLBTDXSSS-UHFFFAOYSA-N
       Ligand Interaction
      CL
      Query on CL

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      AB [auth J] , AC [auth Y] , BB [auth J] , DB [auth K] , FB [auth L] , FC [auth 2] , GB [auth L] , GI [auth 0] , 
      AB [auth J],  AC [auth Y],  BB [auth J],  DB [auth K],  FB [auth L],  FC [auth 2],  GB [auth L],  GI [auth 0],  HI [auth 0],  IB [auth M],  II [auth 0],  JA [auth A],  JB [auth N],  JC [auth 3],  JI [auth 0],  KI [auth 0],  LB [auth O],  LI [auth 0],  MB [auth Q],  PA [auth B],  QB [auth R],  ZA [auth J]
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      MG
      Query on MG

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      AD [auth 0] , AE [auth 0] , AF [auth 0] , BD [auth 0] , BE [auth 0] , BF [auth 0] , CB [auth K] , CD [auth 0] , 
      AD [auth 0],  AE [auth 0],  AF [auth 0],  BD [auth 0],  BE [auth 0],  BF [auth 0],  CB [auth K],  CD [auth 0],  CE [auth 0],  CF [auth 0],  DD [auth 0],  DE [auth 0],  DF [auth 0],  ED [auth 0],  EE [auth 0],  EF [auth 0],  FD [auth 0],  FE [auth 0],  FF [auth 0],  GC [auth 2],  GD [auth 0],  GE [auth 0],  GF [auth 0],  HA [auth A],  HD [auth 0],  HE [auth 0],  HF [auth 0],  IA [auth A],  ID [auth 0],  IE [auth 0],  IF [auth 0],  JD [auth 0],  JE [auth 0],  JF [auth 0],  KD [auth 0],  KE [auth 0],  KF [auth 0],  LD [auth 0],  LE [auth 0],  LF [auth 0],  MC [auth 0],  MD [auth 0],  ME [auth 0],  MF [auth 0],  NC [auth 0],  ND [auth 0],  NE [auth 0],  NF [auth 0],  OA [auth B],  OC [auth 0],  OD [auth 0],  OE [auth 0],  OF [auth 0],  PC [auth 0],  PD [auth 0],  PE [auth 0],  PF [auth 0],  QC [auth 0],  QD [auth 0],  QE [auth 0],  QF [auth 0],  RC [auth 0],  RD [auth 0],  RE [auth 0],  RF [auth 0],  SA [auth C],  SC [auth 0],  SD [auth 0],  SE [auth 0],  TC [auth 0],  TD [auth 0],  TE [auth 0],  UC [auth 0],  UD [auth 0],  UE [auth 0],  UL [auth 9],  VB [auth T],  VC [auth 0],  VD [auth 0],  VE [auth 0],  WC [auth 0],  WD [auth 0],  WE [auth 0],  XC [auth 0],  XD [auth 0],  XE [auth 0],  YC [auth 0],  YD [auth 0],  YE [auth 0],  ZB [auth Y],  ZC [auth 0],  ZD [auth 0],  ZE [auth 0]
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

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      AG [auth 0] , AH [auth 0] , AI [auth 0] , BG [auth 0] , BH [auth 0] , BI [auth 0] , CG [auth 0] , CH [auth 0] , 
      AG [auth 0],  AH [auth 0],  AI [auth 0],  BG [auth 0],  BH [auth 0],  BI [auth 0],  CG [auth 0],  CH [auth 0],  CI [auth 0],  DG [auth 0],  DH [auth 0],  DI [auth 0],  EB [auth L],  EG [auth 0],  EH [auth 0],  EI [auth 0],  FG [auth 0],  FH [auth 0],  FI [auth 0],  GG [auth 0],  GH [auth 0],  HB [auth M],  HG [auth 0],  HH [auth 0],  IG [auth 0],  IH [auth 0],  JG [auth 0],  JH [auth 0],  KG [auth 0],  KH [auth 0],  LG [auth 0],  LH [auth 0],  MG [auth 0],  MH [auth 0],  NA [auth B],  NB [auth Q],  NG [auth 0],  NH [auth 0],  OB [auth R],  OG [auth 0],  OH [auth 0],  PB [auth R],  PG [auth 0],  PH [auth 0],  QG [auth 0],  QH [auth 0],  RG [auth 0],  RH [auth 0],  SG [auth 0],  SH [auth 0],  TA [auth C],  TB [auth S],  TG [auth 0],  TH [auth 0],  UA [auth D],  UF [auth 0],  UG [auth 0],  UH [auth 0],  VF [auth 0],  VG [auth 0],  VH [auth 0],  VL [auth 9],  WF [auth 0],  WG [auth 0],  WH [auth 0],  XF [auth 0],  XG [auth 0],  XH [auth 0],  YA [auth J],  YF [auth 0],  YG [auth 0],  YH [auth 0],  ZF [auth 0],  ZG [auth 0],  ZH [auth 0]
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.245 
      • R-Value Work: 0.194 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 211.316α = 90
      b = 297.905β = 90
      c = 573.138γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data collection
      HKL-2000data reduction
      HKL-2000data scaling
      CNSphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2008-09-23
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Non-polymer description, Version format compliance
      • Version 1.2: 2017-10-25
        Changes: Refinement description