6LUI | pdb_00006lui

Crystal structure of the SAMD1 WH domain and DNA complex

• PDB DOI: https://doi.org/10.2210/pdb6LUI/pdb
• NAKB: 6LUI

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-29 Released: 2021-02-03 
• Deposition Author(s): Zhou, Y., Cao, Y., Wang, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands.

Stielow, B., Zhou, Y., Cao, Y., Simon, C., Pogoda, H.M., Jiang, J., Ren, Y., Phanor, S.K., Rohner, I., Nist, A., Stiewe, T., Hammerschmidt, M., Shi, Y., Bulyk, M.L., Wang, Z., Liefke, R.

(2021) Sci Adv 7

• PubMed: 33980486 
• DOI: https://doi.org/10.1126/sciadv.abf2229
• Primary Citation Related Structures: 
  6LUI, 6LUJ, 6LUK


• PubMed Abstract: 
  

  CpG islands (CGIs) are key regulatory DNA elements at most promoters, but how they influence the chromatin status and transcription remains elusive. Here, we identify and characterize SAMD1 (SAM domain-containing protein 1) as an unmethylated CGI-binding protein. SAMD1 has an atypical winged-helix domain that directly recognizes unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. The SAM domain interacts with L3MBTL3, but it can also homopolymerize into a closed pentameric ring. At a genome-wide level, SAMD1 localizes to H3K4me3-decorated CGIs, where it acts as a repressor. SAMD1 tethers L3MBTL3 to chromatin and interacts with the KDM1A histone demethylase complex to modulate H3K4me2 and H3K4me3 levels at CGIs, thereby providing a mechanism for SAMD1-mediated transcriptional repression. The absence of SAMD1 impairs ES cell differentiation processes, leading to misregulation of key biological pathways. Together, our work establishes SAMD1 as a newly identified chromatin regulator acting at unmethylated CGIs.

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Organizational Affiliation: 
• Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany.
Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China.
Institute of Zoology, University of Cologne, Cologne, Germany.
Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, 35043 Marburg, Germany.
Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Boston, Harvard Medical School, Boston, MA 02115, USA.
Ludwig Institute for Cancer Research, Oxford University, Oxford, UK.
Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China. [e-mail] [e-mail].
Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany. [e-mail] [e-mail].
Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany.

Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 17.48 kDa 
• Atom Count: 1,228 
• Modeled Residue Count: 97 
• Deposited Residue Count: 106 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Atherin	A	80	Homo sapiens	Mutation(s): 0  Gene Names: SAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6SPF0 (Homo sapiens) Explore Q6SPF0  Go to UniProtKB:  Q6SPF0
PHAROS:  Q6SPF0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*CP*TP*GP*CP*GP*CP*AP*CP*CP*AP*T)-3')	B	13	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*GP*TP*GP*CP*GP*CP*AP*GP*GP*T)-3')	C	13	Homo sapiens

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.925	α = 90
b = 45.925	β = 90
c = 132.638	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Zhou, Y., Cao, Y., Wang, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870725
National Natural Science Foundation of China (NSFC)	China	31570729

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary