1VQN

The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 

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
  • Primary Citation of Related Structures:  

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2P
A
240Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl2
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20276
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3P
B
338Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl3
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20279
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4E
C
246Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl4
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12735
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5P
D
177Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl5
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14124
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6P
E
178Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl6
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14135
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7AE
F
120Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl7ae
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12743
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG
G
348Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl10 (rpl10e, rplP0)
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P15825
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L10E
H
171Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl10e
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60617
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13P
J
145Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl13
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P29198
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14P
K
132Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl14
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22450
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15P
L
165Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl15
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12737
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L15E
M
194Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl15e
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60618
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18P
N
187Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl18
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14123
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18e
O
116Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl18e
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12733
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19E
P
149Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl19e
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14119
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21e
Q
96Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl21e
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12734
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22P
R
155Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl22
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10970
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23P
S
85Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl23
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12732
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24P
T
120Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl24
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10972
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24E
U
66Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl24e
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29P
V
71Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl29
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10971
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30P
W
154Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl30
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14121
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31e
X
92Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl31e
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P18138
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32E
Y
241Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl32e
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12736
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37Ae
Z
83Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl37ae
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P60619
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37e
1
57Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl37e
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32410
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e
2
50Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl39e
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22452
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44E
3
92Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl44e
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32411
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11P
I
162Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl11
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14122
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal rna02922Haloarcula marismortui
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA9122Haloarcula marismortui
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*CP*CP*(PPU)*(LOF))-3'44N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-R(*CP*CP*AP*(PHE)*(ACA)*(BTN))-3'56N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
0
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA
Download SDF File 
Download CCD File 
0, 9, C, D, J, M, Q, R, S
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
0, 3, A, B, J, L, M, N, O, R, Y
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
0, 2, 5, 9, A, K, T, Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR
Download SDF File 
Download CCD File 
0, 1, 3, 9, A, B, F, H, L, R, S
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD
Download SDF File 
Download CCD File 
1, 3, O, U, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  9 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
0
RNA LINKINGC9 H13 N2 O9 PU
ACA
Query on ACA
5
PEPTIDE LINKINGC6 H13 N O2

--

OMU
Query on OMU
0
RNA LINKINGC10 H15 N2 O9 PU
1MA
Query on 1MA
0
RNA LINKINGC11 H16 N5 O7 PA
HFA
Query on HFA
4
L-PEPTIDE LINKINGC9 H10 O3

--

BTN
Query on BTN
5
NON-POLYMERC10 H16 N2 O3 S

--

UR3
Query on UR3
0
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
0
RNA LINKINGC11 H16 N5 O8 PG
PPU
Query on PPU
4
RNA LINKINGC22 H30 N7 O8 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 211.721α = 90.00
b = 298.782β = 90.00
c = 575.272γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance