1UKL

Crystal structure of Importin-beta and SREBP-2 complex

• PDB DOI: https://doi.org/10.2210/pdb1UKL/pdb

• Classification: PROTEIN TRANSPORT/DNA BINDING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2003-08-26 Released: 2003-12-09 
• Deposition Author(s): Lee, S.J., Sekimoto, T., Yamashita, E., Nagoshi, E., Nakagawa, A., Imamoto, N., Yoshimura, M., Sakai, H., Tsukihara, T., Yoneda, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.297 
• R-Value Work: 0.239 

Starting Models: experimental

Literature

The Structure of Importin-beta Bound to SREBP-2: Nuclear Import of a Transcription Factor

Lee, S.J., Sekimoto, T., Yamashita, E., Nagoshi, E., Nakagawa, A., Imamoto, N., Yoshimura, M., Sakai, H., Chong, K.T., Tsukihara, T., Yoneda, Y.

(2003) Science 302: 1571-1575

• PubMed: 14645851 
• DOI: https://doi.org/10.1126/science.1088372
• Primary Citation of Related Structures:  
  1UKL


• PubMed Abstract: 
  

  The sterol regulatory element-binding protein 2 (SREBP-2), a nuclear transcription factor that is essential for cholesterol metabolism, enters the nucleus through a direct interaction of its helix-loop-helix leucine zipper domain with importin-beta. We show the crystal structure of importin-beta complexed with the active form of SREBP-2. Importin-beta uses characteristic long helices like a pair of chopsticks to interact with an SREBP-2 dimer. Importin-beta changes its conformation to reveal a pseudo-twofold symmetry on its surface structure so that it can accommodate a symmetric dimer molecule. Importin-beta may use a similar strategy to recognize other dimeric cargoes.

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Organizational Affiliation: 

Institute for Protein Research, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 223.65 kDa 
• Atom Count: 15,606 
• Modelled Residue Count: 1,996 
• Deposited Residue Count: 1,996 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin beta-1 subunit	A, B	876	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P70168 (Mus musculus) Explore P70168  Go to UniProtKB:  P70168

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sterol regulatory element binding protein-2	C, D, E, F	61	Homo sapiens	Mutation(s): 3
UniProt & NIH Common Fund Data Resources
Find proteins for Q12772 (Homo sapiens) Explore Q12772  Go to UniProtKB:  Q12772
PHAROS:  Q12772 GTEx:  ENSG00000198911

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.297 
• R-Value Work: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.092	α = 90
b = 113.285	β = 90
c = 240.044	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-09 
Deposition Author(s): Lee, S.J., Sekimoto, T., Yamashita, E., Nagoshi, E., Nakagawa, A., Imamoto, N., Yoshimura, M., Sakai, H., Tsukihara, T., Yoneda, Y.

Revision History  

• Version 1.0: 2003-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-23
  Changes: Structure summary