3DWH

Structural and Functional Analysis of SRA domain

• PDB DOI: https://doi.org/10.2210/pdb3DWH/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-22 Released: 2008-10-21 
• Deposition Author(s): Qian, C., Jakoncic, J., Zhou, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.253 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Structure and Hemimethylated CpG Binding of the SRA Domain from Human UHRF1.

Qian, C., Li, S., Jakoncic, J., Zeng, L., Walsh, M.J., Zhou, M.M.

(2008) J Biol Chem 283: 34490-34494

• PubMed: 18945682 
• DOI: https://doi.org/10.1074/jbc.C800169200
• Primary Citation of Related Structures:  
  3DWH


• PubMed Abstract: 
  

  Human UHRF1 (ubiquitin-like PHD and RING finger 1) functions to maintain CpG DNA methylation patterns through DNA replication by co-localizing with the DNA methyltransferase DNMT1 at chromatin in mammals. Recent studies show that UHRF1 binds selectively to hemimethylated CpG via its conserved SRA (SET- and RING finger-associated) domain. However, the underlying molecular mechanism is not known. Here, we report a 1.95 A resolution crystal structure of the SRA domain of human UHRF1. Using NMR structure-guided mutagenesis, electrophoretic mobility shift assay, and fluorescence anisotropy analysis, we determined key amino acid residues for methyl-DNA binding that are conserved in the SRA domain.

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Organizational Affiliation: 

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 23.44 kDa 
• Atom Count: 1,662 
• Modelled Residue Count: 193 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A	208	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens) Explore Q96T88  Go to UniProtKB:  Q96T88
PHAROS:  Q96T88 GTEx:  ENSG00000276043

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.253 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.557	α = 90
b = 65.557	β = 90
c = 95.362	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Qian, C., Jakoncic, J., Zhou, M.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-03-13
  Changes: Source and taxonomy, Structure summary