Crystal Structure of the SRAP Domain of Human HMCES Protein

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1038/s41594-019-0246-6
  • Primary Citation of 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.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein277Homo 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
GTEx:  ENSG00000183624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96FZ2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth A]
B [auth A]
BA [auth A]
C [auth A]
CA [auth A]
AA [auth A],
B [auth A],
BA [auth A],
C [auth A],
CA [auth A],
D [auth A],
DA [auth A],
E [auth A],
EA [auth A],
F [auth A],
FA [auth A],
G [auth A],
GA [auth A],
H [auth A],
HA [auth A],
I [auth A],
IA [auth A],
J [auth A],
JA [auth A],
K [auth A],
KA [auth A],
L [auth A],
LA [auth A],
M [auth A],
MA [auth A],
N [auth A],
NA [auth A],
O [auth A],
OA [auth A],
P [auth A],
PA [auth A],
Q [auth A],
QA [auth A],
R [auth A],
RA [auth A],
S [auth A],
SA [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.102α = 90
b = 44.745β = 107.15
c = 82.901γ = 90
Software Package:
Software NamePurpose
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2019-11-13
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description