1Q7Y

Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transferase center of the 50S ribosomal subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Insights Into Peptide Bond Formation

Hansen, J.L.Schmeing, T.M.Moore, P.B.Steitz, T.A.

(2002) Proc Natl Acad Sci U S A 99: 11670-11675

  • DOI: 10.1073/pnas.172404099
  • Primary Citation of Related Structures:  
    1M90, 1Q86, 1Q82, 1Q81, 1Q7Y

  • PubMed Abstract: 
  • The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit ...

    The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2PD [auth C]239Haloarcula 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: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3PE [auth D]337Haloarcula 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: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4EF [auth E]246Haloarcula 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: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5PG [auth F]176Haloarcula 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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6PH [auth G]177Haloarcula 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: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeI [auth H]119Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Acidic ribosomal protein P0 homologJ [auth I]348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
L10 Ribosomal ProteinK [auth J]167Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13PL [auth K]145Haloarcula 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: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14PM [auth L]132Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15PN [auth M]164Haloarcula marismortuiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
L15 Ribosomal ProteinO [auth N]194Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18PP [auth O]186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18eQ [auth P]115Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19ER [auth Q]148Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21eS [auth R]95Haloarcula marismortuiMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22PT [auth S]154Haloarcula 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: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PU [auth T]84Haloarcula marismortuiMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24PV [auth U]119Haloarcula 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: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24EW [auth V]66Haloarcula 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: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29PX [auth W]70Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PY [auth X]154Haloarcula marismortuiMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31eZ [auth Y]91Haloarcula 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: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32EAA [auth Z]240Haloarcula 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: 28
MoleculeChainsSequence LengthOrganismDetailsImage
L37Ae 50S ribosomal proteinBA [auth 1]73Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L37eCA [auth 2]56Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L39eDA [auth 3]48Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L44EEA [auth 4]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal rnaA2922Haloarcula marismortui
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB122Haloarcula marismortui
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  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    CCdA-P-PuromycinC [auth 5]3N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 7 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PUY
    Query on PUY

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    WH [auth 5]PUROMYCIN
    C22 H29 N7 O5
    RXWNCPJZOCPEPQ-NVWDDTSBSA-N
     Ligand Interaction
    CD
    Query on CD

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    AJ [auth 1], BJ [auth 2], DJ [auth 4], NI [auth P], WI [auth V]CADMIUM ION
    Cd
    WLZRMCYVCSSEQC-UHFFFAOYSA-N
     Ligand Interaction
    PO4
    Query on PO4

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    VH [auth 5]PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    K
    Query on K

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    KE [auth A], LE [auth A]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    CL
    Query on CL

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    AI [auth D] , EJ [auth 4] , FI [auth K] , GH [auth A] , GI [auth K] , HH [auth A] , HI [auth K] , IH [auth A] , 
    AI [auth D],  EJ [auth 4],  FI [auth K],  GH [auth A],  GI [auth K],  HH [auth A],  HI [auth K],  IH [auth A],  JH [auth A],  KH [auth A],  LH [auth A],  LI [auth N],  MH [auth A],  MI [auth O],  NH [auth A],  OH [auth A],  OI [auth P],  PH [auth A],  QH [auth A],  TI [auth S],  YI [auth Z],  ZH [auth C]
    CHLORIDE ION
    Cl
    VEXZGXHMUGYJMC-UHFFFAOYSA-M
     Ligand Interaction
    MG
    Query on MG

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    AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , BB [auth A] , BC [auth A] , BD [auth A] , BE [auth A] , 
    AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CJ [auth 4],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  II [auth L],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RH [auth B],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UH [auth 5],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VI [auth U],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XH [auth C],  XI [auth Z],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZI [auth 1]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

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    AF [auth A] , AG [auth A] , AH [auth A] , BF [auth A] , BG [auth A] , BH [auth A] , BI [auth E] , CF [auth A] , 
    AF [auth A],  AG [auth A],  AH [auth A],  BF [auth A],  BG [auth A],  BH [auth A],  BI [auth E],  CF [auth A],  CG [auth A],  CH [auth A],  CI [auth J],  DF [auth A],  DG [auth A],  DH [auth A],  DI [auth J],  EF [auth A],  EG [auth A],  EH [auth A],  EI [auth K],  FF [auth A],  FG [auth A],  FH [auth A],  GF [auth A],  GG [auth A],  HF [auth A],  HG [auth A],  IF [auth A],  IG [auth A],  JF [auth A],  JG [auth A],  JI [auth M],  KF [auth A],  KG [auth A],  KI [auth N],  LF [auth A],  LG [auth A],  ME [auth A],  MF [auth A],  MG [auth A],  NE [auth A],  NF [auth A],  NG [auth A],  OE [auth A],  OF [auth A],  OG [auth A],  PE [auth A],  PF [auth A],  PG [auth A],  PI [auth R],  QE [auth A],  QF [auth A],  QG [auth A],  QI [auth S],  RE [auth A],  RF [auth A],  RG [auth A],  RI [auth S],  SE [auth A],  SF [auth A],  SG [auth A],  SH [auth B],  SI [auth S],  TE [auth A],  TF [auth A],  TG [auth A],  TH [auth B],  UE [auth A],  UF [auth A],  UG [auth A],  UI [auth T],  VE [auth A],  VF [auth A],  VG [auth A],  WE [auth A],  WF [auth A],  WG [auth A],  XE [auth A],  XF [auth A],  XG [auth A],  YE [auth A],  YF [auth A],  YG [auth A],  YH [auth C],  ZE [auth A],  ZF [auth A],  ZG [auth A]
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.280 
    • R-Value Work: 0.225 
    • R-Value Observed: 0.225 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 212.902α = 90
    b = 300.474β = 90
    c = 575.176γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2003-10-07
      Type: Initial release
    • Version 1.1: 2008-04-01
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-01-31
      Changes: Experimental preparation