6FVB | pdb_00006fvb

Structure of Lph2 , a novel bidirectional nuclear transport receptor in S. cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb6FVB/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-01 Released: 2019-09-11 
• Deposition Author(s): Vera Rodriguez, A., Huyton, T., Gorlich, D.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Structure of Lph2 , a novel bidirectional nuclear transport receptor in S. cerevisiae

Vera Rodriguez, A., Huyton, T., Gorlich, D.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 120.45 kDa 
• Atom Count: 8,189 
• Modeled Residue Count: 1,001 
• Deposited Residue Count: 1,031 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin beta-like protein KAP120	A	1,031	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: KAP120, YPL125W
UniProt
Find proteins for Q02932 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02932  Go to UniProtKB:  Q02932

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.851	α = 90
b = 139.851	β = 90
c = 148.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
CRANK2	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Vera Rodriguez, A., Huyton, T., Gorlich, D.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB860

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary