6XTE | pdb_00006xte

Human karyopherin RanBP5 (isoform-1)

• PDB DOI: https://doi.org/10.2210/pdb6XTE/pdb

• Classification: TRANSLOCASE
• Organism(s): Homo sapiens, Actinomycetes
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-01-16 Released: 2020-04-22 
• Deposition Author(s): Swale, C., McCarthy, A.A., Ruigrok, R.W.H., Crepin, T.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.260 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

X-ray Structure of the Human Karyopherin RanBP5, an Essential Factor for Influenza Polymerase Nuclear Trafficking.

Swale, C., Da Costa, B., Sedano, L., Garzoni, F., McCarthy, A.A., Berger, I., Bieniossek, C., Ruigrok, R.W.H., Delmas, B., Crepin, T.

(2020) J Mol Biology 432: 3353-3359

• PubMed: 32222384 
• DOI: https://doi.org/10.1016/j.jmb.2020.03.021
• Primary Citation Related Structures: 
  6XTE, 6XU2


• PubMed Abstract: 
  

  Here, we describe the crystal structures of two distinct isoforms of ligand-free human karyopherin RanBP5 and investigate its global propensity to interact with influenza A virus polymerase. Our results confirm the general architecture and mechanism of the IMB3 karyopherin-β subfamily whilst also highlighting differences with the yeast orthologue Kap121p. Moreover, our results provide insight into the structural flexibility of β-importins in the unbound state. Based on docking of a nuclear localisation sequence, point mutations were designed, which suppress influenza PA-PB1 subcomplex binding to RanBP5 in a binary protein complementation assay.

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Organizational Affiliation: 
• Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France; EMBL Grenoble Outstation, 71 Avenue des Martyrs, BP181, F-38042 Grenoble Cedex 9, France.
Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
EMBL Grenoble Outstation, 71 Avenue des Martyrs, BP181, F-38042 Grenoble Cedex 9, France.
EMBL Grenoble Outstation, 71 Avenue des Martyrs, BP181, F-38042 Grenoble Cedex 9, France; Max Planck Centre for Minimal Biology, University of Bristol, Clifton BS8 1TD, United Kingdom.
Roche Innovation Centre, Basel, Switzerland F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland.
Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.
Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France. Electronic address: [e-mail].

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 124.46 kDa 
• Atom Count: 8,565 
• Modeled Residue Count: 1,079 
• Deposited Residue Count: 1,100 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin-5	A	1,096	Homo sapiens	Mutation(s): 0  Gene Names: IPO5, KPNB3, RANBP5
UniProt & NIH Common Fund Data Resources
Find proteins for O00410 (Homo sapiens) Explore O00410  Go to UniProtKB:  O00410
PHAROS:  O00410 GTEx:  ENSG00000065150

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antipain	B [auth C]	4	Actinomycetes	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
RGL	B [auth C]	L-PEPTIDE LINKING	C6 H15 N4 O		ARG

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000180	B [auth C]	Antipain	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.260 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.091	α = 90
b = 96.313	β = 90
c = 156.979	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Swale, C., McCarthy, A.A., Ruigrok, R.W.H., Crepin, T.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-14-CE09-0017

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2020-05-27
  Changes: Database references
• Version 2.0: 2022-12-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary