1TOV | pdb_00001tov

Structural genomics of Caenorhabditis elegans: CAP-GLY domain of F53F4.3

• PDB DOI: https://doi.org/10.2210/pdb1TOV/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-15 Released: 2004-07-27 
• Deposition Author(s): Li, S., Finley, J., Liu, Z.J., Qiu, S.H., Luan, C.H., Carson, M., Tsao, J., Johnson, D., Lin, G., Zhao, J., Thomas, W., Nagy, L.A., Sha, B., Delucas, L.J., Richardson, D., Richardson, J., Wang, B.C., Luo, M., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal Structure of the Cytoskeleton-Associated Protein Glycine-Rich (CAP-Gly) Domain

Li, S., Finley, J., Liu, Z.J., Qiu, S.H., Luan, C.H., Carson, M., Tsao, J., Johnson, D., Lin, G., Zhao, J., Thomas, W., Nagy, L.A., Sha, B., Delucas, L.J., Wang, B.C., Luo, M.

(2002) J Biological Chem 277: 48596-48601

• PubMed: 12221106 
• DOI: https://doi.org/10.1074/jbc.M208512200
• Primary Citation Related Structures: 
  1LPL, 1TOV


• PubMed Abstract: 
  

  Cytoskeleton-associated proteins (CAPs) are involved in the organization of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of the CAP-Gly domain of Caenorhabditis elegans F53F4.3 protein, solved by single wavelength sulfur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove.

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Organizational Affiliation: 
• Southeast Collaboratory for Structural Genomics, University of Georgia, Athens 30602, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.83 kDa 
• Atom Count: 826 
• Modeled Residue Count: 98 
• Deposited Residue Count: 98 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein F53F4.3 in chromosome V	A	98	Caenorhabditis elegans	Mutation(s): 0  Gene Names: F53F4.3
UniProt
Find proteins for Q20728 (Caenorhabditis elegans) Explore Q20728  Go to UniProtKB:  Q20728

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.156	α = 90
b = 64.156	β = 90
c = 101.946	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
ISAS2001	model building
REFMAC	refinement
HKL-2000	data scaling
ISAS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-27 
Deposition Author(s): Li, S., Finley, J., Liu, Z.J., Qiu, S.H., Luan, C.H., Carson, M., Tsao, J., Johnson, D., Lin, G., Zhao, J., Thomas, W., Nagy, L.A., Sha, B., Delucas, L.J., Richardson, D., Richardson, J., Wang, B.C., Luo, M., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations