2J8Q

Crystal structure of human cleavage and polyadenylation specificity factor 5 (CPSF5) in complex with a sulphate ion.

• PDB DOI: https://doi.org/10.2210/pdb2J8Q/pdb

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


• Deposited: 2006-10-27 Released: 2006-11-13 
• Deposition Author(s): Moche, M., Stenmark, P., Ogg, D., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg, S.L., Hogbom, M., Johansson, I., Karlberg, T., Kosinska, U., Kotenyova, T., Magnusdottir, A., Nilsson, M.E., Nilsson-Ehle, P., Nyman, T., Persson, C., Sagemark, J., Sundstrom, M., Uppenberg, J., Upsten, M., Thorsell, A.G., Van Den Berg, S., Wallden, K., Weigelt, J., Welin, M., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Starting Model: experimental

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 of 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: 53.03 kDa 
• Atom Count: 3,419 
• Modelled Residue Count: 398 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 5	A, B	227	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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.4	α = 90
b = 86.4	β = 90
c = 139.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-13 
Deposition Author(s): Moche, M., Stenmark, P., Ogg, D., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg, S.L., Hogbom, M., Johansson, I., Karlberg, T., Kosinska, U., Kotenyova, T., Magnusdottir, A., Nilsson, M.E., Nilsson-Ehle, P., Nyman, T., Persson, C., Sagemark, J., Sundstrom, M., Uppenberg, J., Upsten, M., Thorsell, A.G., Van Den Berg, S., Wallden, K., Weigelt, J., Welin, M., Nordlund, P.

Revision History  

• Version 1.0: 2006-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description