3UPU | pdb_00003upu

Crystal structure of the T4 Phage SF1B Helicase Dda

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.258 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

The T4 Phage SF1B Helicase Dda Is Structurally Optimized to Perform DNA Strand Separation.

He, X., Byrd, A.K., Yun, M.K., Pemble, C.W., Harrison, D., Yeruva, L., Dahl, C., Kreuzer, K.N., Raney, K.D., White, S.W.

(2012) Structure 20: 1189-1200

  • DOI: https://doi.org/10.1016/j.str.2012.04.013
  • Primary Citation Related Structures: 
    3UPU

  • PubMed Abstract: 

    Helicases move on DNA via an ATP binding and hydrolysis mechanism coordinated by well-characterized helicase motifs. However, the translocation along single-stranded DNA (ssDNA) and the strand separation of double-stranded (dsDNA) may be loosely or tightly coupled. Dda is a phage T4 SF1B helicase with sequence homology to the Pif1 family of helicases that tightly couples translocation to strand separation. The crystal structure of the Dda-ssDNA binary complex reveals a domain referred to as the "pin" that was previously thought to remain static during strand separation. The pin contains a conserved phenylalanine that mediates a transient base-stacking interaction that is absolutely required for separation of dsDNA. The pin is secured at its tip by protein-protein interactions through an extended SH3 domain thereby creating a rigid strut. The conserved interface between the pin and the SH3 domain provides the mechanism for tight coupling of translocation to strand separation.

    • Organizational Affiliation: 
    • Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.

Macromolecule Content 

  • Total Structure Weight: 164.65 kDa 
  • Atom Count: 11,054 
  • Modeled Residue Count: 1,341 
  • Deposited Residue Count: 1,401 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicase dda
A, B, C
459Tequatrovirus T4Mutation(s): 1 
Gene Names: dda, sud
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for P32270 (Enterobacteria phage T4)
Explore P32270 
Go to UniProtKB:  P32270
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32270
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*TP*TP*TP*TP*TP*TP*TP*T)-3'
D, E, F
8N/A
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.258 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.536α = 90
b = 107.253β = 94.128
c = 85.475γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary