5UWU

Crystal Structure of SMAD4 NES Peptide in complex with CRM1-Ran-RanBP1

• PDB DOI:  https://doi.org/10.2210/pdb5UWU/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens, Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-21 Released: 2017-03-22 
• Deposition Author(s): Fung, H.Y.J., Chook, Y.M.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), Croucher Foundation, Cancer Prevention and Research Institute of Texas (CPRIT), Welch Foundation, Leukemia & Lymphoma Society, University of Texas Southwestern

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Literature

Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals.

Fung, H.Y., Fu, S.C., Chook, Y.M.

(2017) Elife 6

• PubMed: 28282025 
• DOI: https://doi.org/10.7554/eLife.23961
• Primary Citation of Related Structures:  
  5UWH, 5UWI, 5UWJ, 5UWO, 5UWP, 5UWQ, 5UWR, 5UWS, 5UWT, 5UWU, 5UWW


• PubMed Abstract: 
  

Nuclear export receptor CRM1 binds highly variable nuclear export signals (NESs) in hundreds of different cargoes. Previously we have shown that CRM1 binds NESs in both polypeptide orientations (Fung et al., 2015). Here, we show crystal structures of CRM1 bound to eight additional NESs which reveal diverse conformations that range from loop-like to all-helix, which occupy different extents of the invariant NES-binding groove. Analysis of all NES structures show 5-6 distinct backbone conformations where the only conserved secondary structural element is one turn of helix that binds the central portion of the CRM1 groove. All NESs also participate in main chain hydrogen bonding with human CRM1 Lys568 side chain, which acts as a specificity filter that prevents binding of non-NES peptides. The large conformational range of NES backbones explains the lack of a fixed pattern for its 3-5 hydrophobic anchor residues, which in turn explains the large array of peptide sequences that can function as NESs.

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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: 163.65 kDa 
• Atom Count: 11,641 
• Modelled Residue Count: 1,345 
• Deposited Residue Count: 1,424 
• 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran-specific GTPase-activating protein 1	B	143	Saccharomyces cerevisiae	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	Mutation(s): 0  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
Mothers against decapentaplegic homolog 4	D	20	Homo sapiens	Mutation(s): 0  Gene Names: SMAD4, DPC4, MADH4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13485 (Homo sapiens) Explore Q13485  Go to UniProtKB:  Q13485
PHAROS:  Q13485

Small Molecules

Ligands 4 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], H [auth C], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.385	α = 90
b = 106.385	β = 90
c = 304.222	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Fung, H.Y.J., Chook, Y.M.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	International Student Research Fellowship
Croucher Foundation	Hong Kong	Predoc Research Scholarship
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP120352, RP150053
Welch Foundation	United States	I-1532
Leukemia & Lymphoma Society	United States	Scholar Award
University of Texas Southwestern	United States	Endowed Scholars Program
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP120352, RP150053

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-04-24
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence