5VE8 | pdb_00005ve8

Crystal structure of full-length Kluyveromyces lactis Kap123 with histone H3 1-28

• PDB DOI: https://doi.org/10.2210/pdb5VE8/pdb

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


• Deposited: 2017-04-04 Released: 2017-11-01 
• Deposition Author(s): An, S., Yoon, J., Song, J.-J., Cho, U.-S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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 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.
Structural Biology Laboratory of Epigenetics, Department of Biological Sciences, Graduate school of Nanoscience and Technology (World Class University), KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.

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: isothermal titration calorimetry, immunoprecipitation, light scattering

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 253.05 kDa 
• Atom Count: 16,129 
• Modeled Residue Count: 2,078 
• Deposited Residue Count: 2,288 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kap123	A, B	1,116	Kluyveromyces lactis	Mutation(s): 0
UniProt
Find proteins for Q6CMF0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CMF0  Go to UniProtKB:  Q6CMF0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C, D [auth E]	28	Kluyveromyces lactis	Mutation(s): 0
UniProt
Find proteins for P61831 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P61831  Go to UniProtKB:  P61831

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: 2.70 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.098	α = 79.59
b = 88.114	β = 80.77
c = 102.276	γ = 70.74

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-13
  Changes: Structure summary