Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 28-mer - A1BCDEFGHIJKLMNOPQRSTUVWXYZab 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1467.16 kDa 
• Atom Count: 98648 
• Residue Count: 6589 
• Unique protein chains: 28
• Unique nucleic acid chains: 3

1QVF

Structure of a deacylated tRNA minihelix bound to the E site of the large ribosomal subunit of Haloarcula marismortui

• DOI: 10.2210/pdb1QVF/pdb
• NDB: RR0080

• Classification: RIBOSOME
• Organism(s): Haloarcula marismortui
• Mutation(s): No 


• Deposited: 2003-08-27 Released: 2003-11-11 
• Deposition Author(s): Schmeing, T.M., Moore, P.B., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 

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

• PubMed: 14561884 
• DOI: 10.1261/rna.5120503
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L2P	A	239	Haloarcula marismortui	Mutation(s): 0
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P20276  Go to UniProtKB:  P20276

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L3P	B	337	Haloarcula marismortui	Mutation(s): 0
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P20279  Go to UniProtKB:  P20279

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L4E	C	246	Haloarcula marismortui	Mutation(s): 0
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12735  Go to UniProtKB:  P12735

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L5P	D	176	Haloarcula marismortui	Mutation(s): 0
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14124  Go to UniProtKB:  P14124

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L6P	E	177	Haloarcula marismortui	Mutation(s): 0
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14135  Go to UniProtKB:  P14135

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L7Ae	F	119	Haloarcula marismortui	Mutation(s): 0
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12743  Go to UniProtKB:  P12743

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L10E	G	348	Haloarcula marismortui	Mutation(s): 0
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P15825  Go to UniProtKB:  P15825

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L13P	I	145	Haloarcula marismortui	Mutation(s): 0
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P29198  Go to UniProtKB:  P29198

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L14P	J	132	Haloarcula marismortui	Mutation(s): 0
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P22450  Go to UniProtKB:  P22450

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L15P	K	164	Haloarcula marismortui	Mutation(s): 0
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12737  Go to UniProtKB:  P12737

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
L15 Ribosomal Protein	L	194	Haloarcula marismortui	Mutation(s): 0
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P60618  Go to UniProtKB:  P60618

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18P	M	186	Haloarcula marismortui	Mutation(s): 0
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14123  Go to UniProtKB:  P14123

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18e	N	115	Haloarcula marismortui	Mutation(s): 0
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12733  Go to UniProtKB:  P12733

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L19E	O	148	Haloarcula marismortui	Mutation(s): 0
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14119  Go to UniProtKB:  P14119

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L21e	P	95	Haloarcula marismortui	Mutation(s): 0
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12734  Go to UniProtKB:  P12734

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L22P	Q	154	Haloarcula marismortui	Mutation(s): 0
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10970  Go to UniProtKB:  P10970

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L23P	R	84	Haloarcula marismortui	Mutation(s): 0
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12732  Go to UniProtKB:  P12732

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24P	S	119	Haloarcula marismortui	Mutation(s): 0
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10972  Go to UniProtKB:  P10972

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L29P	U	70	Haloarcula marismortui	Mutation(s): 0
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10971  Go to UniProtKB:  P10971

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L30P	V	154	Haloarcula marismortui	Mutation(s): 0
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14121  Go to UniProtKB:  P14121

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L31e	W	91	Haloarcula marismortui	Mutation(s): 0
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P18138  Go to UniProtKB:  P18138

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L32E	X	240	Haloarcula marismortui	Mutation(s): 0
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12736  Go to UniProtKB:  P12736

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
L37Ae 50S ribosomal protein	Y	73	Haloarcula marismortui	Mutation(s): 0
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P60619  Go to UniProtKB:  P60619

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L39e	1	48	Haloarcula marismortui	Mutation(s): 0
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P22452  Go to UniProtKB:  P22452

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L44E	2	92	Haloarcula marismortui	Mutation(s): 0
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P32411  Go to UniProtKB:  P32411

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
L10 Ribosomal Protein	H	167	Haloarcula marismortui	Mutation(s): 0
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P60617  Go to UniProtKB:  P60617

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24E	T	66	Haloarcula marismortui	Mutation(s): 0
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14116  Go to UniProtKB:  P14116

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L37e	Z	56	Haloarcula marismortui	Mutation(s): 0
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P32410  Go to UniProtKB:  P32410

Entity ID: 3
Molecule	Chains	Length	Organism
Deacylated tRNA minihelix	3	28	N/A

Entity ID: 1
Molecule	Chains	Length	Organism
23S ribosomal rna	0	2922	Haloarcula marismortui

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	2, N, T, Y, Z	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
K	0	POTASSIUM ION K NPYPAHLBTDXSSS-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, Y	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	0, 9, A, C, H, I, K, L, P, Q, R	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.522	α = 90
b = 300.817	β = 90
c = 574.861	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	refinement
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-27 
• Released Date: 2003-11-11 
Deposition Author(s): Schmeing, T.M., Moore, P.B., Steitz, T.A.

Revision History 

• 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: 2017-11-29
  Changes: Database references