5VCH

Crystal structure of full-length Kluyveromyces lactis Kap123

• PDB DOI:  https://doi.org/10.2210/pdb5VCH/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Kluyveromyces lactis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-31 Released: 2017-11-01 
• Deposition Author(s): An, S., Yoon, J., Song, J.-J., Cho, U.-S.
• Funding Organization(s): American Diabetes Association, March of dimes, National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.235 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123.

An, S., Yoon, J., Kim, H., Song, J.J., Cho, U.S.

(2017) Elife 6

• PubMed: 29035199 
• DOI: https://doi.org/10.7554/eLife.30244
• Primary Citation of Related Structures:  
  5VCH, 5VE8, 5W0V


• PubMed Abstract: 
  

Kap123, a major karyopherin protein of budding yeast, recognizes the nuclear localization signals (NLSs) of cytoplasmic histones H3 and H4 and translocates them into the nucleus during DNA replication. Mechanistic questions include H3- and H4-NLS redundancy toward Kap123 and the role of the conserved diacetylation of cytoplasmic H4 (K5ac and K12ac) in Kap123-mediated histone nuclear translocation. Here, we report crystal structures of full-length Kluyveromyces lactis Kap123 alone and in complex with H3- and H4-NLSs. Structures reveal the unique feature of Kap123 that possesses two discrete lysine-binding pockets for NLS recognition. Structural comparison illustrates that H3- and H4-NLSs share at least one of two lysine-binding pockets, suggesting that H3- and H4-NLSs are mutually exclusive. Additionally, acetylation of key lysine residues at NLS, particularly H4-NLS diacetylation, weakens the interaction with Kap123. These data support that cytoplasmic histone H4 diacetylation weakens the Kap123-H4-NLS interaction thereby facilitating histone Kap123-H3-dependent H3:H4/Asf1 complex nuclear translocation.

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Organizational Affiliation: 

Department of Biological Chemistry, University of Michigan Medical School, Michigan, United States.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 247.06 kDa 
• Atom Count: 16,249 
• Modelled Residue Count: 2,047 
• Deposited Residue Count: 2,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kap123	A, B	1,116	Kluyveromyces lactis	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.235 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.05	α = 79.19
b = 88.12	β = 80.03
c = 102.01	γ = 70.98

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXDE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): An, S., Yoon, J., Song, J.-J., Cho, U.-S.

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Funding Organization	Location	Grant Number
American Diabetes Association	United States	1-16-JDF-017
March of dimes	United States	N019154-00
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG050903
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK111465

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2022-03-16
  Changes: Author supporting evidence, Database references