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: 99.49 kDa 
• Atom Count: 6491 
• Modelled Residue Count: 819 
• Deposited Residue Count: 883 
• Unique protein chains: 3

2X0L

Crystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1.

• DOI: 10.2210/pdb2X0L/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-12-15 Released: 2010-03-02 
• Deposition Author(s): Zibetti, C., Adamo, A., Binda, C., Forneris, F., Verpelli, C., Ginelli, E., Mattevi, A., Sala, C., Battaglioli, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

Alternative Splicing of the Histone Demethylase Lsd1/Kdm1 Contributes to the Modulation of Neurite Morphogenesis in the Mammalian Nervous System.

Zibetti, C., Adamo, A., Binda, C., Forneris, F., Toffolo, E., Verpelli, C., Ginelli, E., Mattevi, A., Sala, C., Battaglioli, E.

(2010) J Neurosci 30: 2521

• PubMed: 20164337 
• DOI: 10.1523/JNEUROSCI.5500-09.2010
• Primary Citation of Related Structures:  
  2X0L


• PubMed Abstract: 
  

A variety of chromatin remodeling complexes are thought to orchestrate transcriptional programs that lead neuronal precursors from earliest commitment to terminal differentiation. Here we show that mammalian neurons have a specialized chromatin remodeling enzyme arising from a neurospecific splice variant of LSD1/KDM1, histone lysine specific demethylase 1, whose demethylase activity on Lys4 of histone H3 has been related to gene repression. We found that alternative splicing of LSD1 transcript generates four full-length isoforms from combinatorial retention of two identified exons: the 4 aa exon E8a is internal to the amine oxidase domain, and its inclusion is restricted to the nervous system. Remarkably, the expression of LSD1 splice variants is dynamically regulated throughout cortical development, particularly during perinatal stages, with a progressive increase of LSD1 neurospecific isoforms over the ubiquitous ones. Notably, the same LSD1 splice dynamics can be fairly recapitulated in cultured cortical neurons. Functionally, LSD1 isoforms display in vitro a comparable demethylase activity, yet the inclusion of the sole exon E8a reduces LSD1 repressor activity on a reporter gene. Additional distinction among isoforms is supported by the knockdown of neurospecific variants in cortical neurons resulting in the inhibition of neurite maturation, whereas overexpression of the same variants enhances it. Instead, perturbation of LSD1 isoforms that are devoid of the neurospecific exon elicits no morphogenic effect. Collectively, results demonstrate that the arousal of neuronal LSD1 isoforms pacemakes early neurite morphogenesis, conferring a neurospecific function to LSD1 epigenetic activity.

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Organizational Affiliation: 

Department of Biology and Genetics for Medical Sciences, University of Milan, 20122 Milan, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC HISTONE DEMETHYLASE 1	A	734	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.99.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
PHAROS:  O60341 GTEx:  ENSG00000004487

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REST COREPRESSOR 1	B	133	Homo sapiens	Mutation(s): 0  Gene Names: RCOR1, KIAA0071, RCOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKL0 (Homo sapiens) Explore Q9UKL0  Go to UniProtKB:  Q9UKL0
PHAROS:  Q9UKL0 GTEx:  ENSG00000089902

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3 PEPTIDE	C	16	Homo sapiens	Mutation(s): 1  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409ENSG00000197153ENSG00000278828ENSG00000275714ENSG00000273983ENSG00000274750ENSG00000275379ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.69	α = 90
b = 181.21	β = 90
c = 233.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-15 
• Released Date: 2010-03-02 
Deposition Author(s): Zibetti, C., Adamo, A., Binda, C., Forneris, F., Verpelli, C., Ginelli, E., Mattevi, A., Sala, C., Battaglioli, E.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Database references, Refinement description, Source and taxonomy, Structure summary, Version format compliance