6WC6 | pdb_00006wc6

Crystal structure of a truncated LSD1:CoREST in the presence of an LSD1-NT peptide

• PDB DOI: https://doi.org/10.2210/pdb6WC6/pdb

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


• Deposited: 2020-03-29 Released: 2021-06-30 
• Deposition Author(s): Reiter, N.J., Zeng, D., Senanayaka, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Identification of structure and nucleosome binding within the N-terminus of lysine specific demethylase 1

Zeng, D., Senanayaka, D., Brown, B.P., Luka, Z., Martin, W.J., Moore, K.I., Patel, R., Pakhomova, S., Meiler, J., Reiter, N.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 92.02 kDa 
• Atom Count: 6,470 
• Modeled Residue Count: 814 
• Deposited Residue Count: 814 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1A	A	666	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1 (PDB Primary Data), 1.14.11 (UniProt), 1.14.99.66 (UniProt), 1.14.11.65 (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
LSD1-NT peptide	C	15	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1.14.11 (UniProt), 1.14.99.66 (UniProt), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O60341 (Homo sapiens) Explore O60341  Go to UniProtKB:  O60341
PHAROS:  O60341 GTEx:  ENSG00000004487

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.783	α = 90
b = 179.164	β = 90
c = 234.907	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Reiter, N.J., Zeng, D., Senanayaka, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM120572

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Advisory, Data collection, Database references, Refinement description