6OEA | pdb_00006oea

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

• PDB DOI: https://doi.org/10.2210/pdb6OEA/pdb
• Entry: 6OEA supersedes: 6NLC
• NAKB: 6OEA

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-27 Released: 2019-04-10 
• Deposition Author(s): Halabelian, L., Ravichandran, M., Li, Y., Zeng, H., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.242 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

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

• PubMed: 31235913 
• DOI: https://doi.org/10.1038/s41594-019-0246-6
• Primary Citation Related Structures: 
  5KO9, 6OE7, 6OEA, 6OEB


• 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. 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
Department of Pharmacology, University of San Diego, La Jolla, CA, USA.
Moores Cancer Center, University of San Diego, La Jolla, CA, USA.
Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada. [e-mail].
Department of Medical Biophysics, University of Toronto, Toronto, Onatario, Canada. [e-mail].
Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 37.48 kDa 
• Atom Count: 2,457 
• Modeled Residue Count: 274 
• Deposited Residue Count: 294 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HMCES, C3orf37, DC12, SRAPD1 EC: 3.4 (PDB Primary Data), 4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FZ2 (Homo sapiens) Explore Q96FZ2  Go to UniProtKB:  Q96FZ2
PHAROS:  Q96FZ2 GTEx:  ENSG00000183624

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*TP*GP*TP*T)-3')	B	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')	C	6	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A], S [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	H [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 B], R [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36oea

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.863	α = 90
b = 52.06	β = 93.11
c = 148.309	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Halabelian, L., Ravichandran, M., Li, Y., Zeng, H., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)
• This entry supersedes: 6NLC

Revision History  

• 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
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description