5YSU

Plumbagin in complex with CRM1-RanM189D-RanBP1

• PDB DOI: https://doi.org/10.2210/pdb5YSU/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-11-15 Released: 2018-11-21 
• Deposition Author(s): Sun, Q., Zhang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Literature

RanL182A in complex with RanBP1-CRM1

Sun, Q., Zhang, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 159.47 kDa 
• Atom Count: 11,387 
• Modelled Residue Count: 1,355 
• Deposited Residue Count: 1,380 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	A	216	Homo sapiens	Mutation(s): 1  Gene Names: RAN, ARA24, OK/SW-cl.81
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens) Explore P62826  Go to UniProtKB:  P62826
PHAROS:  P62826 GTEx:  ENSG00000132341

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran-specific GTPase-activating protein 1	B	140	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41920  Go to UniProtKB:  P41920

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1,Exportin-1	C	1,024	Saccharomyces cerevisiae S288C	Mutation(s): 5  Gene Names: CRM1, KAP124, XPO1, YGR218W, G8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30822  Go to UniProtKB:  P30822

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	D [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
F2X (Subject of Investigation/LOI)	I [auth C], J [auth C]	(2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione C11 H10 O3 ALPCEXCHMFUSAN-ZCFIWIBFSA-N
NO3	G [auth A], H [auth A], M [auth C], N [auth C]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	F [auth A], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.063	α = 90
b = 105.063	β = 90
c = 306.534	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Sun, Q., Zhang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81502629

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description