Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53146.17 
• Atom Count: 3422 
• Residue Count: 396 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1SDS

Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA

• DOI: 10.2210/pdb1SDS/pdb
• NDB: PR0113

• Classification: protein/RNA complex
• Organism(s): Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
• Expression System: Escherichia coli


• Deposited: 2004-02-13 Released: 2004-05-18 
• Deposition Author(s): Hamma, T., Ferre-D'Amare, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.225 
• R-Value Work: 0.207 

Literature

Structure of Protein L7Ae Bound to a K-Turn Derived from an Archaeal Box H/ACA sRNA at 1.8 A Resolution.

Hamma, T., Ferre-D'Amare, A.

(2004) STRUCTURE 12: 893-903

• PubMed: 15130481 
• DOI: 10.1016/j.str.2004.03.015


• PubMed Abstract: 
  

The archaeal RNA binding protein L7Ae and its eukaryotic homolog 15.5 kDa/Snu13 recognize K-turns. This structural motif is canonically comprised of two stems (one with tandem A.G base pairs, the other with Watson-Crick pairs) linked by an asymmetric internal loop. L7Ae recognizes conventional K-turns in ribosomal and box C/D RNAs but also binds specifically to some box H/ACA RNAs at terminal stem loops. These have the A.G paired stem, but lack the Watson-Crick stem. The structure of Methanococcus jannaschii L7Ae bound to a symmetric duplex RNA without Watson-Crick stems demonstrates how a binding site for this component of diverse ribonucleoprotein complexes can be constructed with only the A.G stem and the loop. The RNA adopts a functional conformation with the aid of a base triple and tight binding of divalent cations. Comparison with the 15.5 kDa/Snu13-RNA complex structure suggests why the eukaryotic homolog does not recognize terminal stem loop L7Ae binding sites.

---

Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L7Ae	A, B, C	117	Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)	Mutation(s): 0  Gene Names: rpl7ae
Find proteins for P54066 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Go to UniProtKB:  P54066

Entity ID: 1
Molecule	Chains	Length	Organism
box H/ACA sRNA	D,E,F	15	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	E	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CA	D, E, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.225 
• R-Value Work: 0.207 
• Space Group: F 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 106.970	α = 90.00
b = 141.300	β = 90.00
c = 162.870	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-13 
• Released Date: 2004-05-18 
• Deposition Author(s): Hamma, T., Ferre-D'Amare, A.

Revision History 

• Version 1.0: 2004-05-18
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-11-16
  Type: Atomic model
• Version 1.4: 2018-01-31
  Type: Experimental preparation