1JJ2

Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The kink-turn: a new RNA secondary structure motif.

Klein, D.J.Schmeing, T.M.Moore, P.B.Steitz, T.A.

(2001) EMBO J 20: 4214-4221

  • DOI: https://doi.org/10.1093/emboj/20.15.4214
  • Primary Citation of Related Structures:  
    1JJ2

  • PubMed Abstract: 

    Analysis of the Haloarcula marismortui large ribosomal subunit has revealed a common RNA structure that we call the kink-turn, or K-turn. The six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7 A. There are two K-turns in the structure of Thermus thermophilus 16S rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns. The structure has a kink in the phosphodiester backbone that causes a sharp turn in the RNA helix. Its asymmetric internal loop is flanked by C-G base pairs on one side and sheared G-A base pairs on the other, with an A-minor interaction between these two helical stems. A derived consensus secondary structure for the K-turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5'-UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2C [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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3D [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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L4E [auth C]246Haloarcula 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5F [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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L6G [auth E]177Haloarcula 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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L7AEH [auth F]119Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10I [auth G]348Haloarcula 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: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10EJ [auth H]167Haloarcula 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: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L13K [auth I]145Haloarcula 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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L14L [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: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15M [auth K]164Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15EN [auth L]194Haloarcula 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: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18O [auth M]186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18EP [auth N]115Haloarcula 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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L19EQ [auth O]148Haloarcula 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: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L21ER [auth P]95Haloarcula 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: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L22S [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: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L23T [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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24U [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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24EV [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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L29W [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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L30X [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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L31EY [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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L32EZ [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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37AeAA [auth Y]73Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37EBA [auth Z]56Haloarcula 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: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L39ECA [auth 1]48Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L44EDA [auth 2]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S RRNAA [auth 0]2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S RRNAB [auth 9]122Haloarcula marismortui
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
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AJ [auth 2],
LI [auth N],
UI [auth T],
XI [auth Y],
YI [auth Z]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
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JE [auth 0],
KE [auth 0]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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BJ [auth 2]
CI [auth I]
DI [auth I]
EI [auth I]
FH [auth 0]
BJ [auth 2],
CI [auth I],
DI [auth I],
EI [auth I],
FH [auth 0],
GH [auth 0],
HH [auth 0],
HI [auth K],
IH [auth 0],
JH [auth 0],
JI [auth L],
KH [auth 0],
KI [auth M],
LH [auth 0],
MH [auth 0],
MI [auth N],
NH [auth 0],
OH [auth 0],
QI [auth Q],
VH [auth A],
WI [auth X],
XH [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CE [auth 0],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DE [auth 0],
EA [auth 0],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EE [auth 0],
FA [auth 0],
FB [auth 0],
FC [auth 0],
FD [auth 0],
FE [auth 0],
FI [auth J],
GA [auth 0],
GB [auth 0],
GC [auth 0],
GD [auth 0],
GE [auth 0],
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],
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],
PH [auth 9],
QA [auth 0],
QB [auth 0],
QC [auth 0],
QD [auth 0],
RA [auth 0],
RB [auth 0],
RC [auth 0],
RD [auth 0],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SD [auth 0],
SH [auth A],
SI [auth S],
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],
VA [auth 0],
VB [auth 0],
VC [auth 0],
VD [auth 0],
VI [auth X],
WA [auth 0],
WB [auth 0],
WC [auth 0],
WD [auth 0],
WH [auth B],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XD [auth 0],
YA [auth 0],
YB [auth 0],
YC [auth 0],
YD [auth 0],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0],
ZD [auth 0],
ZI [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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AF [auth 0]
AG [auth 0]
AH [auth 0]
AI [auth H]
BF [auth 0]
AF [auth 0],
AG [auth 0],
AH [auth 0],
AI [auth H],
BF [auth 0],
BG [auth 0],
BH [auth 0],
BI [auth I],
CF [auth 0],
CG [auth 0],
CH [auth 0],
DF [auth 0],
DG [auth 0],
DH [auth 0],
EF [auth 0],
EG [auth 0],
EH [auth 0],
FF [auth 0],
FG [auth 0],
GF [auth 0],
GG [auth 0],
GI [auth K],
HF [auth 0],
HG [auth 0],
IF [auth 0],
IG [auth 0],
II [auth L],
JF [auth 0],
JG [auth 0],
KF [auth 0],
KG [auth 0],
LE [auth 0],
LF [auth 0],
LG [auth 0],
ME [auth 0],
MF [auth 0],
MG [auth 0],
NE [auth 0],
NF [auth 0],
NG [auth 0],
NI [auth P],
OE [auth 0],
OF [auth 0],
OG [auth 0],
OI [auth Q],
PE [auth 0],
PF [auth 0],
PG [auth 0],
PI [auth Q],
QE [auth 0],
QF [auth 0],
QG [auth 0],
QH [auth 9],
RE [auth 0],
RF [auth 0],
RG [auth 0],
RH [auth 9],
RI [auth R],
SE [auth 0],
SF [auth 0],
SG [auth 0],
TE [auth 0],
TF [auth 0],
TG [auth 0],
TI [auth S],
UE [auth 0],
UF [auth 0],
UG [auth 0],
UH [auth A],
VE [auth 0],
VF [auth 0],
VG [auth 0],
WE [auth 0],
WF [auth 0],
WG [auth 0],
XE [auth 0],
XF [auth 0],
XG [auth 0],
YE [auth 0],
YF [auth 0],
YG [auth 0],
YH [auth C],
ZE [auth 0],
ZF [auth 0],
ZG [auth 0],
ZH [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.66α = 90
b = 299.67β = 90
c = 573.77γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations