1LPL | pdb_00001lpl

Structural Genomics of Caenorhabditis elegans: CAP-Gly domain of F53F4.3

• PDB DOI: https://doi.org/10.2210/pdb1LPL/pdb

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


• Deposited: 2002-05-08 Released: 2002-05-22 
• 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., 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: 
  0.297 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.216 (DCC) 

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: 10.36 kDa 
• Atom Count: 813 
• Modeled Residue Count: 95 
• Deposited Residue Count: 95 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 25.4 kDa protein F53F4.3 in chromosome V	A	95	Caenorhabditis elegans	Mutation(s): 0  Gene Names: F53F4.3
UniProt
Find proteins for Q20728 (Caenorhabditis elegans) Explore Q20728  Go to UniProtKB:  Q20728

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.297 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.216 (DCC) 

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
X-PLOR	refinement
HKL-2000	data scaling
ISAS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-22 
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., Wang, B.-C., Luo, M., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2002-05-22
  Type: Initial release
  
• Version 1.1: 2008-04-28
  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