3CME

The Structure of CA and CCA-PHE-CAP-BIO Bound to the Large Ribosomal Subunit of Haloarcula Marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 

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This is version 2.0 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: https://doi.org/10.1261/rna.1118908
  • Primary Citation of Related Structures:  
    3CMA, 3CME

  • 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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2P240Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3P338Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4P246Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5P177Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6P178Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7Ae120Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10E348Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10e177Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11P162Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13P145Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P132Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15P165Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15e196Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18P187Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18e116Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19e149Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21e96Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22P155Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23P85Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24P120Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24e67Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29P71Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30P154Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31e92Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32e240Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37Ae116Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eBA [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44ECA [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains LengthOrganismImage
50S RIBOSOMAL RNADA [auth 0]2,923Haloarcula marismortui
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Entity ID: 31
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAEA [auth 9]122Haloarcula marismortui
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Entity ID: 32
MoleculeChains LengthOrganismImage
RNA (5'-R(*C*CP*A)-3')FA [auth 5]3synthetic construct
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Entity ID: 33
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*(8AN))-3')GA [auth 6]3synthetic construct
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

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AM [auth 6]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
ACA
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BM [auth 6]6-AMINOHEXANOIC ACID
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
CD
Query on CD

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BC [auth Z],
CC [auth 1],
HC [auth 3],
LB [auth O],
WB [auth U]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SR
Query on SR

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AJ [auth 0]
AK [auth 0]
AL [auth 0]
BJ [auth 0]
BK [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],
GC [auth 3],
GJ [auth 0],
GK [auth 0],
GL [auth 0],
HB [auth L],
HJ [auth 0],
HK [auth 0],
HL [auth 0],
IJ [auth 0],
IK [auth 0],
IL [auth 0],
JC [auth 3],
JJ [auth 0],
JK [auth 0],
JL [auth 0],
KC [auth 3],
KI [auth 0],
KJ [auth 0],
KK [auth 0],
KL [auth 0],
LA [auth A],
LI [auth 0],
LJ [auth 0],
LK [auth 0],
LL [auth 0],
MA [auth A],
MI [auth 0],
MJ [auth 0],
MK [auth 0],
ML [auth 0],
NA [auth A],
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],
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],
SA [auth B],
SI [auth 0],
SJ [auth 0],
SK [auth 0],
SL [auth 0],
TB [auth T],
TI [auth 0],
TJ [auth 0],
TK [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],
WI [auth 0],
WJ [auth 0],
WK [auth 0],
XA [auth H],
XB [auth Y],
XI [auth 0],
XJ [auth 0],
XK [auth 0],
XL [auth 9],
YA [auth H],
YI [auth 0],
YJ [auth 0],
YK [auth 0],
YL [auth 9],
ZI [auth 0],
ZJ [auth 0],
ZK [auth 0],
ZL [auth 9]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
K
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PF [auth 0],
QF [auth 0]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
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AC [auth Y]
BB [auth J]
CB [auth J]
DB [auth J]
EI [auth 0]
AC [auth Y],
BB [auth J],
CB [auth J],
DB [auth J],
EI [auth 0],
FB [auth L],
FI [auth 0],
GB [auth L],
GI [auth 0],
HI [auth 0],
IC [auth 3],
II [auth 0],
JB [auth M],
JI [auth 0],
KA [auth A],
KB [auth N],
MB [auth O],
OB [auth Q],
QA [auth B],
QB [auth R],
ZA [auth J],
ZB [auth Y]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
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AD [auth 0]
AE [auth 0]
AF [auth 0]
BD [auth 0]
BE [auth 0]
AD [auth 0],
AE [auth 0],
AF [auth 0],
BD [auth 0],
BE [auth 0],
BF [auth 0],
CD [auth 0],
CE [auth 0],
CF [auth 0],
DD [auth 0],
DE [auth 0],
DF [auth 0],
EB [auth K],
ED [auth 0],
EE [auth 0],
EF [auth 0],
FC [auth 2],
FD [auth 0],
FE [auth 0],
FF [auth 0],
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],
JA [auth A],
JD [auth 0],
JE [auth 0],
JF [auth 0],
KD [auth 0],
KE [auth 0],
KF [auth 0],
LC [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],
PA [auth B],
PC [auth 0],
PD [auth 0],
PE [auth 0],
QC [auth 0],
QD [auth 0],
QE [auth 0],
RC [auth 0],
RD [auth 0],
RE [auth 0],
SC [auth 0],
SD [auth 0],
SE [auth 0],
TA [auth C],
TC [auth 0],
TD [auth 0],
TE [auth 0],
TL [auth 9],
UC [auth 0],
UD [auth 0],
UE [auth 0],
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],
YB [auth Y],
YC [auth 0],
YD [auth 0],
YE [auth 0],
ZC [auth 0],
ZD [auth 0],
ZE [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AB [auth J]
AG [auth 0]
AH [auth 0]
AI [auth 0]
BG [auth 0]
AB [auth J],
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],
EG [auth 0],
EH [auth 0],
FG [auth 0],
FH [auth 0],
GG [auth 0],
GH [auth 0],
HG [auth 0],
HH [auth 0],
IB [auth M],
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],
NB [auth Q],
NG [auth 0],
NH [auth 0],
OG [auth 0],
OH [auth 0],
PB [auth R],
PG [auth 0],
PH [auth 0],
QG [auth 0],
QH [auth 0],
RF [auth 0],
RG [auth 0],
RH [auth 0],
SB [auth S],
SF [auth 0],
SG [auth 0],
SH [auth 0],
TF [auth 0],
TG [auth 0],
TH [auth 0],
UA [auth C],
UF [auth 0],
UG [auth 0],
UH [auth 0],
UL [auth 9],
VF [auth 0],
VG [auth 0],
VH [auth 0],
VL [auth 9],
WA [auth H],
WF [auth 0],
WG [auth 0],
WH [auth 0],
WL [auth 9],
XF [auth 0],
XG [auth 0],
XH [auth 0],
YF [auth 0],
YG [auth 0],
YH [auth 0],
ZF [auth 0],
ZG [auth 0],
ZH [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.786α = 90
b = 297.778β = 90
c = 572.588γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description, Source and taxonomy
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations