Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 104.77 kDa 
• Atom Count: 6515 
• Modelled Residue Count: 778 
• Deposited Residue Count: 921 
• Unique protein chains: 3

4GUS

Crystal structure of LSD2-NPAC with H3 in space group P3221

• DOI: 10.2210/pdb4GUS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-29 Released: 2013-01-16 
• Deposition Author(s): Chen, F., Dong, Z., Fang, J., Yang, Y., Li, Z., Xu, Y., Yang, H., Wang, P., Fang, R., Shi, Y., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation

Fang, R., Chen, F., Dong, Z., Hu, D., Barbera, A.J., Clark, E.A., Fang, J., Yang, Y., Mei, P., Rutenberg, M., Li, Z., Zhang, Y., Xu, Y., Yang, H., Wang, P., Simon, M.D., Zhou, Q., Li, J., Marynick, M.P., Li, X., Lu, H., Kaiser, U.B., Kingston, R.E., Xu, Y., Shi, Y.G.

(2013) Mol Cell 49: 558-570

• PubMed: 23260659 
• DOI: 10.1016/j.molcel.2012.11.019
• Primary Citation of Related Structures:  
  4GU1, 4GUR, 4GUS, 4GUT, 4GUU


• PubMed Abstract: 
  

Dynamic regulation of histone methylation represents a fundamental epigenetic mechanism underlying eukaryotic gene regulation, yet little is known about how the catalytic activities of histone demethylases are regulated. Here, we identify and characterize NPAC/GLYR1 as an LSD2/KDM1b-specific cofactor that stimulates H3K4me1 and H3K4me2 demethylation. We determine the crystal structures of LSD2 alone and LSD2 in complex with the NPAC linker region in the absence or presence of histone H3 peptide, at resolutions of 2.9, 2.0, and 2.25 Å, respectively. These crystal structures and further biochemical characterization define a dodecapeptide of NPAC (residues 214-225) as the minimal functional unit for its cofactor activity and provide structural determinants and a molecular mechanism underlying the intrinsic cofactor activity of NPAC in stimulating LSD2-catalyzed H3K4 demethylation. Thus, these findings establish a model for how a cofactor directly regulates histone demethylation and will have a significant impact on our understanding of catalytic-activity-based epigenetic regulation.

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Organizational Affiliation: 

Division of Endocrinology, Diabetes, and Hypertension, Department of Medicine and Department of Biological Chemistry & Molecular Pharmacology, Brigham and Women's Hospital and Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1B	A	776	Homo sapiens	Mutation(s): 0  Gene Names: LSD2, KDM1B, AOF1, C6orf193 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NB78 (Homo sapiens) Explore Q8NB78  Go to UniProtKB:  Q8NB78
PHAROS:  Q8NB78 GTEx:  ENSG00000165097

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase GLYR1	B	124	Homo sapiens	Mutation(s): 0  Gene Names: GLYR1, HIBDL, NDF, NP60 EC: 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q49A26 (Homo sapiens) Explore Q49A26  Go to UniProtKB:  Q49A26
PHAROS:  Q49A26 GTEx:  ENSG00000140632

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	C	21	Homo sapiens	Mutation(s): 1  Gene Names: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000163041

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
IOD	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	M [auth A], N [auth A], O [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.083	α = 90
b = 101.083	β = 90
c = 177.372	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2012-08-29 
• Released Date: 2013-01-16 
Deposition Author(s): Chen, F., Dong, Z., Fang, J., Yang, Y., Li, Z., Xu, Y., Yang, H., Wang, P., Fang, R., Shi, Y., Xu, Y.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references