2CL3 | pdb_00002cl3

Crystal structure of human Cleavage and Polyadenylation Specificity Factor 5 (CPSF5)

• PDB DOI: https://doi.org/10.2210/pdb2CL3/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-04-25 Released: 2006-05-04 
• Deposition Author(s): Stenmark, P., Hogbom, M., Arrowsmith, C., Berglund, H., Collins, R., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Kotenyova, T., Magnusdottir, A., Nilsson-Ehle, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Wallden, K., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

The Crystal Structure of Human Cleavage and Polyadenylation Specific Factor-5 Reveals a Dimeric Nudix Protein with a Conserved Catalytic Site.

Tresaugues, L., Stenmark, P., Schuler, H., Flodin, S., Welin, M., Nyman, T., Hammarstrom, M., Moche, M., Graslund, S., Nordlund, P.

(2008) Proteins 73: 1047

• PubMed: 18767156 
• DOI: https://doi.org/10.1002/prot.22198
• Primary Citation Related Structures: 
  2CL3, 2J8Q

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Structural Genomics Consortium, Karolinska Institute, Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 26.72 kDa 
• Atom Count: 1,889 
• Modeled Residue Count: 202 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5	A	230	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43809 (Homo sapiens) Explore O43809  Go to UniProtKB:  O43809
PHAROS:  O43809 GTEx:  ENSG00000167005

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.92	α = 90
b = 79.92	β = 90
c = 72.22	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-04 
Deposition Author(s): Stenmark, P., Hogbom, M., Arrowsmith, C., Berglund, H., Collins, R., Edwards, A., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Kotenyova, T., Magnusdottir, A., Nilsson-Ehle, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Wallden, K., Weigelt, J., Nordlund, P.

Revision History  

• Version 1.0: 2006-05-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other