8QYZ | pdb_00008qyz

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 (Depositor), 0.247 (DCC)
R-Value Work:
0.218 (Depositor), 0.217 (DCC)

Starting Model: experimental
View more details

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
Modeled 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 P [auth B] SDF format, chain S [auth E] SDF format, chain V [auth G] SDF format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth E] MOL2 format, chain V [auth G] MOL2 format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth E] mmCIF format, chain V [auth G] mmCIF format, chain M [auth A]	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] Interactions & Density 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 X [auth G] SDF format, chain U [auth E] SDF format, chain R [auth B] SDF format, chain O [auth A] MOL2 format, chain X [auth G] MOL2 format, chain U [auth E] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] mmCIF format, chain X [auth G] mmCIF format, chain U [auth E] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A]	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] Interactions & Density 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 W [auth G] SDF format, chain T [auth E] SDF format, chain Q [auth B] SDF format, chain N [auth A] MOL2 format, chain W [auth G] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] mmCIF format, chain W [auth G] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A]	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] Interactions & Density Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth E] Focus chain W [auth G]