5DI9

Crystal Structure of hRio2 NES Reverse Mutant Peptide in complex with CRM1-Ran-RanBP1

• PDB DOI: https://doi.org/10.2210/pdb5DI9/pdb

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


• Deposited: 2015-08-31 Released: 2015-09-16 
• Deposition Author(s): Fung, H.Y., Chook, Y.M.
• Funding Organization(s): Croucher Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT), University of Texas Southwestern, Welch Foundation, Leukemia & Lymphoma Society

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.211 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Structural determinants of nuclear export signal orientation in binding to exportin CRM1.

Fung, H.Y., Fu, S.C., Brautigam, C.A., Chook, Y.M.

(2015) Elife 4

• PubMed: 26349033 
• DOI: https://doi.org/10.7554/eLife.10034
• Primary Citation of Related Structures:  
  5DH9, 5DHA, 5DHF, 5DI9, 5DIF


• PubMed Abstract: 
  

  The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). Comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.

---

Organizational Affiliation: 

Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 164.2 kDa 
• Atom Count: 11,370 
• Modelled Residue Count: 1,347 
• Deposited Residue Count: 1,425 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	A	237	Homo sapiens	Mutation(s): 0  Gene Names: RAN, ARA24, OK/SW-cl.81 EC: 3.6.5
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	143	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	C	1,024	Saccharomyces cerevisiae S288C	Mutation(s): 6  Gene Names: CRM1, KAP124, XPO1, YGR218W, G8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30822  Go to UniProtKB:  P30822

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered Nuclear Export Signal Peptide (hRio2 NES reverse mutant)	D	21	Homo sapiens	Mutation(s): 0  Gene Names: CPEB4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
GOL	G [auth A], J [auth C], K [auth C], L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.211 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.692	α = 90
b = 106.692	β = 90
c = 304.497	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Fung, H.Y., Chook, Y.M.

---

Funding Organization	Location	Grant Number
Croucher Foundation	Hong Kong	Student Scholarship
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM069909
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP120352
University of Texas Southwestern	United States	Endowed Scholars Program
Welch Foundation	United States	I-1532
Leukemia & Lymphoma Society	United States	Scholar Award

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence
• Version 1.4: 2019-04-24
  Changes: Author supporting evidence, Data collection
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.7: 2023-11-15
  Changes: Data collection