1JJ2 image
Deposition Date 2001-07-03
Release Date 2001-08-01
Last Version Date 2024-02-07
Entry Detail
PDB ID:
1JJ2
Keywords:
Title:
Fully Refined Crystal Structure of the Haloarcula marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.22
R-Value Work:
0.18
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S RRNA
Chain IDs:A (auth: 0)
Chain Length:2922
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L39E
Gene (Uniprot):rpl39e
Chain IDs:CA (auth: 1)
Chain Length:48
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L44E
Gene (Uniprot):rpl44e
Chain IDs:DA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polyribonucleotide
Molecule:5S RRNA
Chain IDs:B (auth: 9)
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L2
Gene (Uniprot):rpl2
Chain IDs:C (auth: A)
Chain Length:239
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L3
Gene (Uniprot):rpl3
Chain IDs:D (auth: B)
Chain Length:337
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L4
Gene (Uniprot):rpl4
Chain IDs:E (auth: C)
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L5
Gene (Uniprot):rpl5
Chain IDs:F (auth: D)
Chain Length:176
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L6
Gene (Uniprot):rpl6
Chain IDs:G (auth: E)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L7AE
Gene (Uniprot):rpl7ae
Chain IDs:H (auth: F)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L10
Gene (Uniprot):rpl10
Chain IDs:I (auth: G)
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L10E
Chain IDs:J (auth: H)
Chain Length:167
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L13
Gene (Uniprot):rpl13
Chain IDs:K (auth: I)
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L14
Gene (Uniprot):rpl14
Chain IDs:L (auth: J)
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L15
Gene (Uniprot):rpl15
Chain IDs:M (auth: K)
Chain Length:164
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L15E
Chain IDs:N (auth: L)
Chain Length:194
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L18
Gene (Uniprot):rpl18
Chain IDs:O (auth: M)
Chain Length:186
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L18E
Gene (Uniprot):rpl18e
Chain IDs:P (auth: N)
Chain Length:115
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L19E
Gene (Uniprot):rpl19e
Chain IDs:Q (auth: O)
Chain Length:148
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L21E
Gene (Uniprot):rpl21e
Chain IDs:R (auth: P)
Chain Length:95
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L22
Gene (Uniprot):rpl22
Chain IDs:S (auth: Q)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L23
Gene (Uniprot):rpl23
Chain IDs:T (auth: R)
Chain Length:84
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L24
Gene (Uniprot):rpl24
Chain IDs:U (auth: S)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L24E
Gene (Uniprot):rpl24e
Chain IDs:V (auth: T)
Chain Length:66
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpl29
Chain IDs:W (auth: U)
Chain Length:70
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L30
Gene (Uniprot):rpl30
Chain IDs:X (auth: V)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L31E
Gene (Uniprot):rpl31e
Chain IDs:Y (auth: W)
Chain Length:91
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L32E
Gene (Uniprot):rpl32e
Chain IDs:Z (auth: X)
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L37Ae
Chain IDs:AA (auth: Y)
Chain Length:73
Number of Molecules:1
Biological Source:Haloarcula marismortui
Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L37E
Gene (Uniprot):rpl37e
Chain IDs:BA (auth: Z)
Chain Length:56
Number of Molecules:1
Biological Source:Haloarcula marismortui
Primary Citation
The kink-turn: a new RNA secondary structure motif.
EMBO J. 20 4214 4221 (2001)
PMID: 11483524 DOI: 10.1093/emboj/20.15.4214

Abstact

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.

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Primary Citation of related structures