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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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 (RF ...

    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: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3P
B
338Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20279

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5P
D
177Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14124

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10E
G
348Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P15825

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10e
H
177Haloarcula marismortuiMutation(s): 0 
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60617

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11P
I
162Haloarcula marismortuiMutation(s): 0 
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14122

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22P
R
155Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10970

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24P
T
120Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10972

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29P
V
71Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10971

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2P
A
240Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20276

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13P
J
145Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P29198

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14P
K
132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22450

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15P
L
165Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12737

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15e
M
196Haloarcula marismortuiMutation(s): 0 
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60618

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18P
N
187Haloarcula marismortuiMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14123

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18e
O
116Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12733

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19e
P
149Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14119

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21e
Q
96Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12734

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23P
S
85Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12732

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24e
U
67Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30P
W
154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14121

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31e
X
92Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P18138

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32e
Y
240Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12736

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37Ae
Z
116Haloarcula marismortuiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37e
1
57Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32410

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e
2
50Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22452

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44E
3
92Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32411

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4P
C
246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12735

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6P
E
178Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14135

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
F
120Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12743

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Entity ID: 30
MoleculeChainsLengthOrganism
50S RIBOSOMAL RNA02923Haloarcula marismortui

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Entity ID: 31
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNA9122Haloarcula marismortui
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 32
MoleculeChainsLengthOrganism
RNA (5'-R(*C*CP*A)-3')53synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 33
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*(8AN))-3')63synthetic construct
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download CCD File 
6
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
ACA
Query on ACA

Download CCD File 
6
6-AMINOHEXANOIC ACID
C6 H13 N O2
SLXKOJJOQWFEFD-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download CCD File 
1, 3, O, U, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

Download CCD File 
0, 1, 3, 9, A, B, F, H, L, R, T, Y
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
0
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
0, 3, A, B, J, L, M, N, O, Q, R, Y
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
0, 2, 9, A, B, C, K, T, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
0, 9, C, H, J, M, Q, R, S
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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



Entry History 

Deposition Data

Revision History 

  • 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