5YSU | pdb_00005ysu

Plumbagin in complex with CRM1-RanM189D-RanBP1

PDB DOI: https://doi.org/10.2210/pdb5YSU/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-11-15 Released: 2018-11-21
Deposition Author(s): Sun, Q., Zhang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

RanL182A in complex with RanBP1-CRM1

Sun, Q., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 159.47 kDa
Atom Count: 11,387
Modeled Residue Count: 1,355
Deposited Residue Count: 1,380
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	A	216	Homo sapiens	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62826
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ran-specific GTPase-activating protein 1	B	140	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41920
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-1,Exportin-1	C	1,024	Saccharomyces cerevisiae S288C	Mutation(s): 5 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30822
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
F2X (Subject of Investigation/LOI) Query on F2X Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C]	I [auth C], J [auth C]	(2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione C₁₁ H₁₀ O₃ ALPCEXCHMFUSAN-ZCFIWIBFSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain I [auth C] Focus chain J [auth C]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], M [auth C], N [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C] Focus chain N [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain F [auth A]	F [auth A], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain K [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth C]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.063	α = 90
b = 105.063	β = 90
c = 306.534	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Sun, Q.

Zhang, Y.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81502629

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 2.0: 2020-07-29
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-10-23
Changes: Structure summary