1ST0 | pdb_00001st0

Structure of DcpS bound to m7GpppG

• PDB DOI: https://doi.org/10.2210/pdb1ST0/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-03-24 Released: 2004-04-13 
• Deposition Author(s): Gu, M., Fabrega, C., Liu, S.W., Liu, H., Kiledjian, M., Lima, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 

Literature

Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity

Gu, M., Fabrega, C., Liu, S.W., Liu, H., Kiledjian, M., Lima, C.D.

(2004) Mol Cell 14: 67-80

• PubMed: 15068804 
• DOI: https://doi.org/10.1016/s1097-2765(04)00180-7
• Primary Citation Related Structures: 
  1ST0, 1ST4


• PubMed Abstract: 
  

  Complete removal of residual N-7 guanine cap from degraded messenger RNA is necessary to prevent accumulation of intermediates that might interfere with RNA processing, export, and translation. The human scavenger decapping enzyme, DcpS, catalyzes residual cap hydrolysis following mRNA degradation, releasing N-7 methyl guanosine monophosphate and 5'-diphosphate terminated cap or mRNA products. DcpS structures bound to m(7)GpppG or m(7)GpppA reveal an asymmetric DcpS dimer that simultaneously creates an open nonproductive DcpS-cap complex and a closed productive DcpS-cap complex that alternate via 30 A domain movements. Structural and biochemical analysis suggests an autoregulatory mechanism whereby premature decapping mRNA is prevented by blocking the conformational changes that are required to form a closed productive active site capable of cap hydrolysis.

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Organizational Affiliation: 
• Structural Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 79.15 kDa 
• Atom Count: 5,647 
• Modeled Residue Count: 597 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA decapping enzyme	A [auth B], B [auth A]	337	Homo sapiens	Mutation(s): 1  Gene Names: DCPS EC: 3.6.1.59
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C86 (Homo sapiens) Explore Q96C86  Go to UniProtKB:  Q96C86
PHAROS:  Q96C86 GTEx:  ENSG00000110063

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTG	C [auth B], G [auth A]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE C21 H30 N10 O18 P3 FHHZHGZBHYYWTG-INFSMZHSSA-O
YT3	D [auth A], E [auth A], F [auth A]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.446	α = 90
b = 94.783	β = 90
c = 178.328	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-13 
Deposition Author(s): Gu, M., Fabrega, C., Liu, S.W., Liu, H., Kiledjian, M., Lima, C.D.

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection