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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.8 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62826
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41920
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30822
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	G [auth A], J [auth C], K [auth C], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Ligand Structure Quality Assessment

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 (Full details and data files)

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
Version 1.8: 2024-11-20
Changes: Structure summary