8QYZ

Crystal structure of hiNES2 in complex with Xpo1 and RanGTP

PDB DOI: https://doi.org/10.2210/pdb8QYZ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Saccharomyces cerevisiae S288C, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-10-26 Released: 2024-11-06
Deposition Author(s): Rymarenko, O., Huyton, T., Gorlich, D.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.247
R-Value Work: 0.218

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Exploring sequence space and engineering of Xpo1-dependent NESes

Rymarenko, O., Huyton, T., Gorlich, D.

To be published.

Macromolecule Content

Total Structure Weight: 573.43 kDa
Atom Count: 39,266
Modelled Residue Count: 4,810
Deposited Residue Count: 4,984
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein GSP1/CNR1	A, C [auth B], E, G	182	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: GSP1
UniProt
Find proteins for P32835 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32835 Go to UniProtKB: P32835
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32835
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1	B [auth C], D, F, H	1,048	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CRM1
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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hiNES2	I, J, K, L	16	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain S [auth E] SDF format, chain V [auth G] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth E] MOL2 format, chain V [auth G] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth E] mmCIF format, chain V [auth G]	M [auth A], P [auth B], S [auth E], V [auth G]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth E] Focus chain V [auth G]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain U [auth E] SDF format, chain X [auth G] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth E] MOL2 format, chain X [auth G] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth E] mmCIF format, chain X [auth G]	O [auth A], R [auth B], U [auth E], X [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth E] Focus chain X [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth E] SDF format, chain W [auth G] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth E] MOL2 format, chain W [auth G] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth E] mmCIF format, chain W [auth G]	N [auth A], Q [auth B], T [auth E], W [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth E] Focus chain W [auth G]