6OEB

Crystal structure of HMCES SRAP domain in complex with 3' overhang DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.

Halabelian, L.Ravichandran, M.Li, Y.Zeng, H.Rao, A.Aravind, L.Arrowsmith, C.H.

(2019) Nat Struct Mol Biol 26: 607-612

  • DOI: 10.1038/s41594-019-0246-6
  • Primary Citation of Related Structures:  
    5KO9, 6OEA, 6OEB, 6OE7

  • PubMed Abstract: 
  • Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA ...

    Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked with an abasic site within a 3' overhang DNA. HMCES interacts with both single-strand and duplex segments of DNA, with two independent duplex DNA interaction sites identified in the SRAP domain. The HMCES DNA-protein cross-link structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys 2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with a variety of single-strand- and double-strand-containing DNA structures found in DNA-damage sites, including 5' and 3' overhang DNAs and gapped DNAs with short single-strand segments.


    Organizational Affiliation

    Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. cheryl.arrowsmith@uhnresearch.ca.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding proteinA276Homo sapiensMutation(s): 0 
Gene Names: HMCESC3orf37DC12SRAPD1
EC: 3.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FZ2 (Homo sapiens)
Explore Q96FZ2 
Go to UniProtKB:  Q96FZ2
PHAROS:  Q96FZ2
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3')B9synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')C6synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EDO
      Query on EDO

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], T [auth C]1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      UNX
      Query on UNX

      Download Ideal Coordinates CCD File 
      I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , O [auth A] , P [auth A] , 
      I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth B]
      UNKNOWN ATOM OR ION
      X
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 55.728α = 90
      b = 51.151β = 92.77
      c = 149.21γ = 90
      Software Package:
      Software NamePurpose
      Aimlessdata scaling
      REFMACrefinement
      PDB_EXTRACTdata extraction
      XDSdata reduction
      PHASERphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2019-04-10
        Type: Initial release
      • Version 1.1: 2019-06-26
        Changes: Data collection, Database references
      • Version 1.2: 2019-07-10
        Changes: Data collection, Database references
      • Version 1.3: 2019-07-17
        Changes: Data collection, Database references