Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.97 kDa 
• Atom Count: 778 
• Modelled Residue Count: 101 
• Deposited Residue Count: 126 
• Unique protein chains: 1

1SE9

Structure of At3g01050, a ubiquitin-fold protein from Arabidopsis thaliana

• PDB DOI: 10.2210/pdb1SE9/pdb
• BMRB: 6128

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2004-02-16 Released: 2004-02-24 
• Deposition Author(s): Volkman, B.F., Lytle, B.L., Peterson, F.C., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Cell-free protein production and labeling protocol for NMR-based structural proteomics.

Vinarov, D.A., Lytle, B.L., Peterson, F.C., Tyler, E.M., Volkman, B.F., Markley, J.L.

(2004) Nat Methods 1: 149-153

• PubMed: 15782178 
• DOI: 10.1038/nmeth716
• Primary Citation of Related Structures:  
  1SE9


• PubMed Abstract: 
  

Structural proteomics requires robust, scalable methods. Here we describe a wheat germ cell-free platform for protein production that supports efficient NMR structural studies of eukaryotic proteins and offers advantages over cell-based methods. To illustrate this platform, we describe its application to a specific target (At3g01050.1) from Arabidopsis thaliana. After cloning the target gene into a specialized plasmid, we carry out a small-scale (50 mul) in vitro sequential transcription and translation trial to ascertain the level of protein production and solubility. Next, we prepare mRNA for use in a 4-ml semicontinuous cell-free translation reaction to incorporate (15)N-labeled amino acids into a protein sample that we purify and test for suitability for NMR structural analysis. We then repeat the cell-free approach with (13)C,(15)N-labeled amino acids to prepare a doubly labeled sample. The three-dimensional (3D) structure of At3g01050.1 shows that this protein is an unusual member of the beta-grasp protein family.

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Organizational Affiliation: 

Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin family	A	126	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At3g01050, MUB1, T4P13.27
UniProt
Find proteins for Q9MAB9 (Arabidopsis thaliana) Explore Q9MAB9  Go to UniProtKB:  Q9MAB9

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 1SE9 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-02-16 
• Released Date: 2004-02-24 
Deposition Author(s): Volkman, B.F., Lytle, B.L., Peterson, F.C., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2004-02-24
  Type: Initial release
  
• Version 1.1: 2008-02-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Data collection, Database references, Derived calculations