7JJM | pdb_00007jjm

Crystal structure of Importin alpha 2 in complex with LSD1 NLS

• PDB DOI: https://doi.org/10.2210/pdb7JJM/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-27 Released: 2020-08-05 
• Deposition Author(s): Tu, W.J., McGuaig, R., Tan, H.Y.A., Hardy, C., Seddiki, N., Ali, S., Dahlstrom, J.E., Bean, E.G., Dunn, J., Forwood, J.K., Tsimbalyuk, S., Smith, K.M., Yip, D., Malik, L., Prasana, T., Milburn, P., Rao, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Targeting Nuclear LSD1 to Reprogram Cancer Cells and Reinvigorate Exhausted T Cells via a Novel LSD1-EOMES Switch.

Tu, W.J., McCuaig, R.D., Tan, A.H.Y., Hardy, K., Seddiki, N., Ali, S., Dahlstrom, J.E., Bean, E.G., Dunn, J., Forwood, J., Tsimbalyuk, S., Smith, K., Yip, D., Malik, L., Prasanna, T., Milburn, P., Rao, S.

(2020) Front Immunol 11: 1228

• DOI: https://doi.org/10.3389/fimmu.2020.01228

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.15 kDa 
• Atom Count: 3,396 
• Modeled Residue Count: 428 
• Deposited Residue Count: 496 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific histone demethylase 1A	A	26	Homo sapiens	Mutation(s): 0  Gene Names: KDM1A, AOF2, KDM1, KIAA0601, LSD1 EC: 1.14.99.66 (PDB Primary Data), 1.14.11 (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
Importin subunit alpha-1	B	470	Mus musculus	Mutation(s): 0  Gene Names: Kpna2, Rch1
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus) Explore P52293  Go to UniProtKB:  P52293
IMPC:  MGI:103561

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.61	α = 90
b = 90.05	β = 90
c = 99.75	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Tu, W.J., McGuaig, R., Tan, H.Y.A., Hardy, C., Seddiki, N., Ali, S., Dahlstrom, J.E., Bean, E.G., Dunn, J., Forwood, J.K., Tsimbalyuk, S., Smith, K.M., Yip, D., Malik, L., Prasana, T., Milburn, P., Rao, S.

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description