1QVG

Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit

Schmeing, T.M.Moore, P.B.Steitz, T.A.

(2003) RNA 9: 1345-1352

  • DOI: https://doi.org/10.1261/rna.5120503
  • Primary Citation of Related Structures:  
    1QVF, 1QVG

  • PubMed Abstract: 

    During translation, tRNAs cycle through three binding sites on the ribosome: the A, the P, and the E sites. We have determined the structures of complexes between the Haloarcula marismortui large ribosomal subunit and two different E site substrates: a deacylated tRNA acceptor stem minihelix and a CCA-acceptor end. Both of these tRNA mimics contain analogs of adenosine 76, the component responsible for a large proportion of E site binding affinity. They bind in the center of the loop-extension of protein L44e, and make specific contacts with both L44e and 23S rRNA including bases that are conserved in all three kingdoms of life. These contacts are consistent with the footprinting, protection, and cross-linking data that have identified the E site biochemically. These structures explain the specificity of the E site for deacylated tRNAs, as it is too small to accommodate any relevant aminoacyl-tRNA. The orientation of the minihelix suggests that it may mimic the P/E hybrid state. It appears that the E site on the 50S subunit was formed by only RNA in the last common ancestor of the three kingdoms, since the proteins at the E sites of H. marismortui and Deinucoccus radiodurans large subunits are not homologous.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2PF [auth A]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3PG [auth B]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4EH [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PI [auth D]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6PJ [auth E]177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeK [auth F]119Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10EL [auth G]348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
L10 Ribosomal ProteinM [auth H]167Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PN [auth I]145Haloarcula marismortuiMutation(s): 0 
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Find proteins for P29198 (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 L14PO [auth J]132Haloarcula 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: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PP [auth K]164Haloarcula marismortuiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
L15 Ribosomal ProteinQ [auth L]194Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PR [auth M]186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eS [auth N]115Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19ET [auth O]148Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eU [auth P]95Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PV [auth Q]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PW [auth R]84Haloarcula 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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PX [auth S]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24EY [auth T]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PZ [auth U]70Haloarcula 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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PAA [auth V]154Haloarcula 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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31eBA [auth W]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32ECA [auth X]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
MoleculeChains Sequence LengthOrganismDetailsImage
L37Ae 50S ribosomal proteinDA [auth Y]73Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37eEA [auth Z]56Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eFA [auth 1]48Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44EGA [auth 2]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal rnaA [auth 0]2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 9]122Haloarcula marismortui
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Entity ID: 3
MoleculeChains LengthOrganismImage
Oligonucleotide CCAC [auth 3],
D [auth 4],
E [auth 5]
3N/A
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

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AJ [auth Z],
CJ [auth 2],
NI [auth N],
WI [auth T],
ZI [auth Y]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

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KE [auth 0],
LE [auth 0]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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DI [auth I]
DJ [auth 2]
EI [auth I]
FI [auth I]
HH [auth 0]
DI [auth I],
DJ [auth 2],
EI [auth I],
FI [auth I],
HH [auth 0],
HI [auth J],
IH [auth 0],
JH [auth 0],
JI [auth K],
KH [auth 0],
LH [auth 0],
LI [auth L],
MH [auth 0],
MI [auth M],
NH [auth 0],
OH [auth 0],
OI [auth N],
PH [auth 0],
TI [auth Q],
XH [auth A],
YI [auth X],
ZH [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AB [auth 0]
AC [auth 0]
AD [auth 0]
AE [auth 0]
BB [auth 0]
AB [auth 0],
AC [auth 0],
AD [auth 0],
AE [auth 0],
BB [auth 0],
BC [auth 0],
BD [auth 0],
BE [auth 0],
BJ [auth 2],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CE [auth 0],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DE [auth 0],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EE [auth 0],
FB [auth 0],
FC [auth 0],
FD [auth 0],
FE [auth 0],
GB [auth 0],
GC [auth 0],
GD [auth 0],
GE [auth 0],
GI [auth J],
HA [auth 0],
HB [auth 0],
HC [auth 0],
HD [auth 0],
HE [auth 0],
IA [auth 0],
IB [auth 0],
IC [auth 0],
ID [auth 0],
IE [auth 0],
JA [auth 0],
JB [auth 0],
JC [auth 0],
JD [auth 0],
JE [auth 0],
KA [auth 0],
KB [auth 0],
KC [auth 0],
KD [auth 0],
LA [auth 0],
LB [auth 0],
LC [auth 0],
LD [auth 0],
MA [auth 0],
MB [auth 0],
MC [auth 0],
MD [auth 0],
NA [auth 0],
NB [auth 0],
NC [auth 0],
ND [auth 0],
OA [auth 0],
OB [auth 0],
OC [auth 0],
OD [auth 0],
PA [auth 0],
PB [auth 0],
PC [auth 0],
PD [auth 0],
QA [auth 0],
QB [auth 0],
QC [auth 0],
QD [auth 0],
QH [auth 9],
RA [auth 0],
RB [auth 0],
RC [auth 0],
RD [auth 0],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SD [auth 0],
TA [auth 0],
TB [auth 0],
TC [auth 0],
TD [auth 0],
TH [auth A],
UA [auth 0],
UB [auth 0],
UC [auth 0],
UD [auth 0],
UH [auth A],
VA [auth 0],
VB [auth 0],
VC [auth 0],
VD [auth 0],
VH [auth A],
VI [auth S],
WA [auth 0],
WB [auth 0],
WC [auth 0],
WD [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XD [auth 0],
XI [auth X],
YA [auth 0],
YB [auth 0],
YC [auth 0],
YD [auth 0],
YH [auth B],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0],
ZD [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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AF [auth 0]
AG [auth 0]
AH [auth 0]
AI [auth C]
BF [auth 0]
AF [auth 0],
AG [auth 0],
AH [auth 0],
AI [auth C],
BF [auth 0],
BG [auth 0],
BH [auth 0],
BI [auth H],
CF [auth 0],
CG [auth 0],
CH [auth 0],
CI [auth I],
DF [auth 0],
DG [auth 0],
DH [auth 0],
EF [auth 0],
EG [auth 0],
EH [auth 0],
FF [auth 0],
FG [auth 0],
FH [auth 0],
GF [auth 0],
GG [auth 0],
GH [auth 0],
HF [auth 0],
HG [auth 0],
IF [auth 0],
IG [auth 0],
II [auth K],
JF [auth 0],
JG [auth 0],
KF [auth 0],
KG [auth 0],
KI [auth L],
LF [auth 0],
LG [auth 0],
ME [auth 0],
MF [auth 0],
MG [auth 0],
NE [auth 0],
NF [auth 0],
NG [auth 0],
OE [auth 0],
OF [auth 0],
OG [auth 0],
PE [auth 0],
PF [auth 0],
PG [auth 0],
PI [auth P],
QE [auth 0],
QF [auth 0],
QG [auth 0],
QI [auth Q],
RE [auth 0],
RF [auth 0],
RG [auth 0],
RH [auth 9],
RI [auth Q],
SE [auth 0],
SF [auth 0],
SG [auth 0],
SH [auth 9],
SI [auth Q],
TE [auth 0],
TF [auth 0],
TG [auth 0],
UE [auth 0],
UF [auth 0],
UG [auth 0],
UI [auth R],
VE [auth 0],
VF [auth 0],
VG [auth 0],
WE [auth 0],
WF [auth 0],
WG [auth 0],
WH [auth A],
XE [auth 0],
XF [auth 0],
XG [auth 0],
YE [auth 0],
YF [auth 0],
YG [auth 0],
ZE [auth 0],
ZF [auth 0],
ZG [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.517α = 90
b = 300.612β = 90
c = 573.929γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description