1VQ6

The structure of c-hpmn and CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.

Schmeing, T.M.Huang, K.S.Strobel, S.A.Steitz, T.A.

(2005) Nature 438: 520-524

  • DOI: 10.1038/nature04152
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The large ribosomal subunit catalyses the reaction between the alpha-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site, while preventing the nucleophilic attack of water on the ester, ...

    The large ribosomal subunit catalyses the reaction between the alpha-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site, while preventing the nucleophilic attack of water on the ester, which would lead to unprogrammed deacylation of the peptidyl-tRNA. Here we describe three new structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with peptidyl transferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-site residues reposition to allow the peptidyl transferase reaction. Proper binding of an aminoacyl-tRNA analogue to the A site induces specific movements of 23S rRNA nucleotides 2618-2620 (Escherichia coli numbering 2583-2585) and 2541(2506), thereby reorienting the ester group of the peptidyl-tRNA and making it accessible for attack. In the absence of the appropriate A-site substrate, the peptidyl transferase centre positions the ester link of the peptidyl-tRNA in a conformation that precludes the catalysed nucleophilic attack by water. Protein release factors may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis.


    Related Citations: 
    • Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.
      Schmeing, T.M., Huang, K.S., Kitchen, D.E., Strobel, S.A., Steitz, T.A.
      (2005) Mol Cell 20: 437

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.



Macromolecules

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Entity ID: 5
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: 6
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: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4E
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: 8
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: 9
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: 10
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: 11
MoleculeChainsSequence LengthOrganismDetails
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
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: 12
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L10E
H
171Haloarcula 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: 13
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: 14
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: 16
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L15E
M
194Haloarcula 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: 18
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: 19
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: 20
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: 22
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: 23
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: 25
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: 26
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: 27
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: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32E
Y
241Haloarcula 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: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37Ae
Z
83Haloarcula marismortuiMutation(s): 0 
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60619

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Entity ID: 30
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: 31
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: 32
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: 33
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: 15
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: 17
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: 21
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: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24E
U
66Haloarcula 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: 1
MoleculeChainsLengthOrganism
23S ribosomal rna02922Haloarcula marismortui
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Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*CP*(5AA)*(HFA))-3'43N/A
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Entity ID: 4
MoleculeChainsLengthOrganism
5'-R(*CP*CP*AP*(PHE)*(ACA)*(BTN))-3'56N/A

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA9122Haloarcula marismortui
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
1, 3, O, U, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-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, K, L, M, N, O, R, Y
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
0, 3, 5, 9, A, B, K, T, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
0, 9, A, C, H, J, L, M, Q, R, S
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.05α = 90
b = 300.187β = 90
c = 573.987γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance