Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 225.18 kDa 
• Atom Count: 14991 
• Modelled Residue Count: 1863 
• Deposited Residue Count: 1984 
• Unique protein chains: 4

5DIS

Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid FG-repeat containing fragment of Nup214

• PDB DOI: 10.2210/pdb5DIS/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-09-01 Released: 2015-11-04 
• Deposition Author(s): Monecke, T., Port, S.A., Dickmanns, A., Kehlenbach, R.H., Ficner, R.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.249 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Structural and Functional Characterization of CRM1-Nup214 Interactions Reveals Multiple FG-Binding Sites Involved in Nuclear Export.

Port, S.A., Monecke, T., Dickmanns, A., Spillner, C., Hofele, R., Urlaub, H., Ficner, R., Kehlenbach, R.H.

(2015) Cell Rep 13: 690-702

• PubMed: 26489467 
• DOI: 10.1016/j.celrep.2015.09.042
• Primary Citation of Related Structures:  
  5DIS


• PubMed Abstract: 
  

CRM1 is the major nuclear export receptor. During translocation through the nuclear pore, transport complexes transiently interact with phenylalanine-glycine (FG) repeats of multiple nucleoporins. On the cytoplasmic side of the nuclear pore, CRM1 tightly interacts with the nucleoporin Nup214. Here, we present the crystal structure of a 117-amino-acid FG-repeat-containing fragment of Nup214, in complex with CRM1, Snurportin 1, and RanGTP at 2.85 Å resolution. The structure reveals eight binding sites for Nup214 FG motifs on CRM1, with intervening stretches that are loosely attached to the transport receptor. Nup214 binds to N- and C-terminal regions of CRM1, thereby clamping CRM1 in a closed conformation and stabilizing the export complex. The role of conserved hydrophobic pockets for the recognition of FG motifs was analyzed in biochemical and cell-based assays. Comparative studies with RanBP3 and Nup62 shed light on specificities of CRM1-nucleoporin binding, which serves as a paradigm for transport receptor-nucleoporin interactions.

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Related Citations: 

• Combining dehydration, construct optimization and improved data collection to solve the crystal structure of a CRM1-RanGTP-SPN1-Nup214 quaternary export complex
  Monecke, T., Dickmanns, A., Weiss, M.S., Port, S.A., Kehlenbach, R.H., Ficner, R.
  () To be published --: --

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Organizational Affiliation: 

Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1	A	1044	Homo sapiens	Mutation(s): 0  Gene Names: XPO1, CRM1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens) Explore O14980  Go to UniProtKB:  O14980
PHAROS:  O14980

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	B	172	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Snurportin-1	C	289	Homo sapiens	Mutation(s): 0  Gene Names: SNUPN, RNUT1, SPN1
UniProt & NIH Common Fund Data Resources
Find proteins for O95149 (Homo sapiens) Explore O95149  Go to UniProtKB:  O95149
PHAROS:  O95149

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214	D	479	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: malE, b4034, JW3994, NUP214, CAIN, CAN, KIAA0023
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P35658 (Homo sapiens) Explore P35658  Go to UniProtKB:  P35658
PHAROS:  P35658
UniProt Groups	P0AEX9P35658

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	G [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
PRO	F [auth A], I [auth C]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
MG	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	E	alpha-maltose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.249 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.33	α = 90
b = 248.97	β = 90
c = 210.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-09-01 
• Released Date: 2015-11-04 
Deposition Author(s): Monecke, T., Port, S.A., Dickmanns, A., Kehlenbach, R.H., Ficner, R.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB860

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary