Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 28-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZab 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1458155.25 
• Atom Count: 90650 
• Residue Count: 7279 
• Unique protein chains: 28
• Unique nucleic acid chains: 2

1JJ2

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

• DOI: 10.2210/pdb1JJ2/pdb
• NDB: RR0033

• Classification: RIBOSOME
• Organism(s): Haloarcula marismortui, Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)


• Deposited: 2001-07-03 Released: 2001-08-01 
• Deposition Author(s): Klein, D.J., Schmeing, T.M., Moore, P.B., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.222 
• R-Value Work: 0.189 

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

• PubMed: 11483524 
• DOI: 10.1093/emboj/20.15.4214


• 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.

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Related Citations: 

• The Fully Refined Crystal Structure of the H. marismortui 50S Subunit at 2.4 Angstrom Resolution
  Klein, D.J.,Schmeing, T.M.,Nissen, P.,Ban, N.,Moore, P.B.,Steitz, T.A.
  () TO BE PUBLISHED --: --




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L2	A	239	Haloarcula 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: 4
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L3	B	337	Haloarcula 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: 5
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L4	C	246	Haloarcula 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: 6
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L5	D	176	Haloarcula 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: 7
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L6	E	177	Haloarcula 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: 8
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L7AE	F	119	Haloarcula 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: 9
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L10	G	348	Haloarcula 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: 10
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L10E	H	167	Haloarcula 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: 11
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L13	I	145	Haloarcula 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: 12
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L14	J	132	Haloarcula 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: 13
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L15	K	164	Haloarcula 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: 14
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L15E	L	194	Haloarcula 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: 15
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L18	M	186	Haloarcula 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: 16
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L18E	N	115	Haloarcula 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: 17
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L19E	O	148	Haloarcula 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: 18
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L21E	P	95	Haloarcula 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: 19
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L22	Q	154	Haloarcula 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: 20
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L23	R	84	Haloarcula 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: 21
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L24	S	119	Haloarcula 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: 22
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L24E	T	66	Haloarcula 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: 23
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L29	U	70	Haloarcula 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: 24
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L30	V	154	Haloarcula 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: 25
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L31E	W	91	Haloarcula 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: 26
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L32E	X	240	Haloarcula 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: 27
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L37Ae	Y	73	Haloarcula 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: 28
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L37E	Z	56	Haloarcula 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: 29
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L39E	1	48	Haloarcula 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: 30
Molecule	Chains	Sequence Length	Organism	Details
RIBOSOMAL PROTEIN L44E	2	92	Haloarcula 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: 1
Molecule	Chains	Length	Organism
23S RRNA	0	2922	Haloarcula marismortui

Entity ID: 2
Molecule	Chains	Length	Organism
5S RRNA	9	122	Haloarcula marismortui

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	0	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	0, 9, A, C, H, I, K, L, P, Q, R, S	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	0, 2, A, B, I, K, L, M, N, Q, X	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	0, 2, 9, A, B, J, S, X	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
CD	2, N, T, Y, Z	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.222 
• R-Value Work: 0.189 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 211.660	α = 90.00
b = 299.670	β = 90.00
c = 573.770	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	phasing
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-03 
• Released Date: 2001-08-01 
• Deposition Author(s): Klein, D.J., Schmeing, T.M., Moore, P.B., Steitz, T.A.

Revision History 

• Version 1.0: 2001-08-01
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance