6N1Z | pdb_00006n1z

Importin-9 bound to H2A-H2B

• PDB DOI: https://doi.org/10.2210/pdb6N1Z/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Xenopus laevis
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-11-12 Released: 2019-03-20 
• Deposition Author(s): Tomchick, D.R., Chook, Y.M., Padavannil, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.238 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone.

Padavannil, A., Sarkar, P., Kim, S.J., Cagatay, T., Jiou, J., Brautigam, C.A., Tomchick, D.R., Sali, A., D'Arcy, S., Chook, Y.M.

(2019) Elife 8

• PubMed: 30855230 
• DOI: https://doi.org/10.7554/eLife.43630
• Primary Citation Related Structures: 
  6N1Z


• PubMed Abstract: 
  

  We report the crystal structure of nuclear import receptor Importin-9 bound to its cargo, the histones H2A-H2B. Importin-9 wraps around the core, globular region of H2A-H2B to form an extensive interface. The nature of this interface coupled with quantitative analysis of deletion mutants of H2A-H2B suggests that the NLS-like sequences in the H2A-H2B tails play a minor role in import. Importin-9•H2A-H2B is reminiscent of interactions between histones and histone chaperones in that it precludes H2A-H2B interactions with DNA and H3-H4 as seen in the nucleosome. Like many histone chaperones, which prevent inappropriate non-nucleosomal interactions, Importin-9 also sequesters H2A-H2B from DNA. Importin-9 appears to act as a storage chaperone for H2A-H2B while escorting it to the nucleus. Surprisingly, RanGTP does not dissociate Importin-9•H2A-H2B but assembles into a RanGTP•Importin-9•H2A-H2B complex. The presence of Ran in the complex, however, modulates Imp9-H2A-H2B interactions to facilitate its dissociation by DNA and assembly into a nucleosome.

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Organizational Affiliation: 
• Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.
Department of Biological Sciences, University of Texas at Dallas, Richardson, United States.
Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States.
Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United states.
Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 287.66 kDa 
• Atom Count: 18,161 
• Modeled Residue Count: 2,270 
• Deposited Residue Count: 2,588 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin-9	A, D	1,041	Homo sapiens	Mutation(s): 0  Gene Names: IPO9, IMP9, KIAA1192, RANBP9, HSPC273
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P70 (Homo sapiens) Explore Q96P70  Go to UniProtKB:  Q96P70
PHAROS:  Q96P70 GTEx:  ENSG00000198700

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	B, E	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	C, F	123	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.238 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.424	α = 90
b = 223.289	β = 90
c = 131.833	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Tomchick, D.R., Chook, Y.M., Padavannil, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM069909
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM98256-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM083960
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM109824
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM112108
Welch Foundation	United States	I-1532

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references