Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 97.15 kDa 
• Atom Count: 6488 
• Modelled Residue Count: 772 
• Deposited Residue Count: 820 
• Unique protein chains: 3

5KQ4

Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2 and synthetic cap analog

• DOI: 10.2210/pdb5KQ4/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe 972h-, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-05 Released: 2016-10-05 
• Deposition Author(s): Mugridge, J.S., Ziemniak, M., Jemielity, J., Gross, J.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.251 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Structural basis of mRNA-cap recognition by Dcp1-Dcp2.

Mugridge, J.S., Ziemniak, M., Jemielity, J., Gross, J.D.

(2016) Nat Struct Mol Biol 23: 987-994

• PubMed: 27694842 
• DOI: 10.1038/nsmb.3301
• Primary Citation of Related Structures:  
  5KQ1, 5KQ4


• PubMed Abstract: 
  

Removal of the 5' cap on mRNA by the decapping enzyme Dcp2 is a critical step in 5'-to-3' mRNA decay. Understanding the structural basis of Dcp2 activity has been a challenge because Dcp2 is dynamic and has weak affinity for the cap substrate. Here we present a 2.6-Å-resolution crystal structure of a heterotrimer of fission yeast Dcp2, its essential activator Dcp1, and the human NMD cofactor PNRC2, in complex with a tight-binding cap analog. Cap binding is accompanied by a conformational change in Dcp2, thereby forming a composite nucleotide-binding site comprising conserved residues in the catalytic and regulatory domains. Kinetic analysis of PNRC2 revealed that a conserved short linear motif enhances both substrate affinity and the catalytic step of decapping. These findings explain why Dcp2 requires a conformational change for efficient catalysis and reveals that coactivators promote RNA binding and the catalytic step of decapping, possibly through different conformational states.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA-decapping enzyme subunit 1	A, D	130	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: dcp1, SPBC3B9.21
Find proteins for Q9P805 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9P805  Go to UniProtKB:  Q9P805

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline-rich nuclear receptor coactivator 2	C, F	31	Homo sapiens	Mutation(s): 0  Gene Names: PNRC2, HSPC208
Find proteins for Q9NPJ4 (Homo sapiens) Explore Q9NPJ4  Go to UniProtKB:  Q9NPJ4
NIH Common Fund Data Resources
PHAROS:  Q9NPJ4 GTEx:  ENSG00000189266

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA decapping complex subunit 2	B, E	249	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: dcp2, SPAC19A8.12 EC: 3
Find proteins for O13828 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O13828  Go to UniProtKB:  O13828

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6VQ	B, E	[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate C22 H34 N10 O19 P4 S2 SZQMTBAJCPCVLP-BZDQESSTSA-P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.251 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.067	α = 90
b = 120.752	β = 97.9
c = 91.849	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-07-05 
• Released Date: 2016-10-05 
Deposition Author(s): Mugridge, J.S., Ziemniak, M., Jemielity, J., Gross, J.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM078360
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM105313

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2016-11-16
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2017-11-01
  Changes: Author supporting evidence
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence