PDB-8qyz: Crystal structure of hiNES2 in complex with Xpo1 and RanGTP

ID or keywords:

Entry

Database: PDB / ID: 8qyz

Title

Crystal structure of hiNES2 in complex with Xpo1 and RanGTP

Components

Exportin-1
GTP-binding nuclear protein GSP1/CNR1
hiNES2

Keywords

TRANSPORT PROTEIN / NES / Exportin / RanGTP

Function / homology

Function and homology information

regulation of cell cycle phase transition / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of nucleocytoplasmic transport / Postmitotic nuclear pore complex (NPC) reformation / tRNA re-export from nucleus / Transcriptional and post-translational regulation of MITF-M expression and activity / nuclear export signal receptor activity / tRNA export from nucleus / protein localization to kinetochore / U4 snRNA binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae S288C (yeast)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

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

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Exploring sequence space and engineering of Xpo1-dependent NESes
Authors: Rymarenko, O. / Huyton, T. / Gorlich, D.

History

Deposition	Oct 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 6, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qyz.cif.gz	2.5 MB	Display	PDBx/mmCIF format
PDB format	pdb8qyz.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	8qyz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qy/8qyz ftp://data.pdbj.org/pub/pdb/validation_reports/qy/8qyz	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#85 - Jan 2007 Importins similarity (7) #205 - Jan 2017 Nuclear Pore Complex similarity (17) #166 - Oct 2013 Proteasome similarity (1) #161 - May 2013 Ricin similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: GTP-binding nuclear protein GSP1/CNR1

C: Exportin-1

B: GTP-binding nuclear protein GSP1/CNR1

D: Exportin-1

E: GTP-binding nuclear protein GSP1/CNR1

F: Exportin-1

G: GTP-binding nuclear protein GSP1/CNR1

H: Exportin-1

I: hiNES2

J: hiNES2

K: hiNES2

L: hiNES2

hetero molecules

573 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTP-binding nuclear protein GSP1/CNR1

C: Exportin-1

I: hiNES2

hetero molecules

defined by author
Evidence: gel filtration
143 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: GTP-binding nuclear protein GSP1/CNR1

D: Exportin-1

J: hiNES2

hetero molecules

defined by author
143 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: GTP-binding nuclear protein GSP1/CNR1

F: Exportin-1

K: hiNES2

hetero molecules

defined by author
143 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: GTP-binding nuclear protein GSP1/CNR1

H: Exportin-1

L: hiNES2

hetero molecules

defined by author
143 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.355, 105.572, 170.400
Angle α, β, γ (deg.)	82.080, 86.668, 76.668
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	10 - 181
2	1	1	A	10 - 181
3	2	2	A	10 - 178
4	2	2	A	10 - 178
5	3	3	A	10 - 178
6	3	3	A	10 - 178
7	4	4	A	5 - 1055
8	4	4	A	5 - 1055
9	5	5	A	5 - 1054
10	5	5	A	5 - 1054
11	6	6	A	5 - 1054
12	6	6	A	5 - 1054
13	7	7	A	10 - 178
14	7	7	A	10 - 178
15	8	8	A	10 - 178
16	8	8	A	10 - 178
17	9	9	A	5 - 1054
18	9	9	A	5 - 1054
19	10	10	A	5 - 1054
20	10	10	A	5 - 1054
21	11	11	A	10 - 179
22	11	11	A	10 - 179
23	12	12	A	5 - 1056
24	12	12	A	5 - 1056
25	13	13	A	0 - 15
26	13	13	A	0 - 15
27	14	14	A	0 - 15
28	14	14	A	0 - 15
29	15	15	A	0 - 15
30	15	15	A	0 - 15
31	16	16	A	0 - 15
32	16	16	A	0 - 15
33	17	17	A	0 - 15
34	17	17	A	0 - 15
35	18	18	A	0 - 15
36	18	18	A	0 - 15

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36

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Protein , 2 types, 8 molecules ABEGCDFH

#1: Protein	GTP-binding nuclear protein GSP1/CNR1 Mass: 20672.861 Da / Num. of mol.: 4 / Mutation: 1-182, Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: GSP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P32835
#2: Protein	Exportin-1 Mass: 120327.117 Da / Num. of mol.: 4 / Mutation: del(377-413) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: CRM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30822

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Protein/peptide , 1 types, 4 molecules IJKL

#3: Protein/peptide	hiNES2 Mass: 1749.958 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 221 molecules

#4: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: Tris, PEG 20K, magnesium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 20, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→84.36 Å / Num. obs: 126263 / % possible obs: 96.47 % / Redundancy: 3.41 % / CC_1/2: 0.8256 / R_merge(I) obs: 0.1386 / Net I/σ(I): 8.05
Reflection shell	Resolution: 3→3.05 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.995 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6193 / CC_1/2: 0.606 / % possible all: 94.69

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0350	refinement
Coot		model building
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→82.792 Å / Cor.coef. F_o:F_c: 0.921 / Cor.coef. F_o:F_c free: 0.899 / SU B: 52.02 / SU ML: 0.402 / Cross valid method: FREE R-VALUE / ESU R Free: 0.436 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2469	6264	4.962 %
R_work	0.2177	119969	-
all	0.219	-	-
obs	-	126233	96.405 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 79.868 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	-1.416 Å²	2.28 Å²
2-	-	-0.602 Å²	-0.887 Å²
3-	-	-	0.015 Å²

Refinement step

Cycle: LAST / Resolution: 3→82.792 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	38872	0	148	209	39229

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	39847
X-RAY DIFFRACTION	r_angle_refined_deg	1.148	1.632	53983
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.366	5	4806
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	2.747	10	169
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.143	10	7306
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.232	10	1854
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	6238
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	29272
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	21629
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	28044
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	1122
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.356	0.2	146
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.203	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.866	4.556	19252
X-RAY DIFFRACTION	r_mcangle_it	3.145	6.83	24046
X-RAY DIFFRACTION	r_scbond_it	2.122	4.689	20595
X-RAY DIFFRACTION	r_scangle_it	3.527	6.982	29937
X-RAY DIFFRACTION	r_lrange_it	9.011	156.579	1534427
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	5836
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.103	0.05	5575
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.094	0.05	5607
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.084	0.05	36140
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.112	0.05	35058
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.109	0.05	35151
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.097	0.05	5575
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.091	0.05	5593
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.11	0.05	35005
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.106	0.05	35045
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.096	0.05	5616
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.108	0.05	35212
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.131	0.05	413
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.18	0.05	418
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.161	0.05	412
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.178	0.05	405
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.14	0.05	410
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.168	0.05	416

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07265	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07265	0.05011
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10329	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.10329	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09425	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09425	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08435	0.05011
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08435	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.11154	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.11154	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10856	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10856	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.09698	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.09698	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.09065	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.09065	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.10973	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.10973	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.10624	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.10624	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.09587	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.09587	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.10822	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.10822	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.1313	0.05006
13	26	A	X-RAY DIFFRACTION	Local ncs	0.1313	0.05006
14	27	A	X-RAY DIFFRACTION	Local ncs	0.17958	0.05007
14	28	A	X-RAY DIFFRACTION	Local ncs	0.17958	0.05007
15	29	A	X-RAY DIFFRACTION	Local ncs	0.16146	0.05006
15	30	A	X-RAY DIFFRACTION	Local ncs	0.16146	0.05006
16	31	A	X-RAY DIFFRACTION	Local ncs	0.17829	0.05006
16	32	A	X-RAY DIFFRACTION	Local ncs	0.17829	0.05006
17	33	A	X-RAY DIFFRACTION	Local ncs	0.14048	0.05006
17	34	A	X-RAY DIFFRACTION	Local ncs	0.14048	0.05006
18	35	A	X-RAY DIFFRACTION	Local ncs	0.1683	0.05006
18	36	A	X-RAY DIFFRACTION	Local ncs	0.1683	0.05006

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3-3.078	0.355	468	0.334	8740	0.335	9668	0.916	0.924	95.242	0.335
3.078-3.162	0.328	450	0.308	8672	0.309	9424	0.927	0.936	96.7954	0.306
3.162-3.253	0.302	459	0.288	8428	0.289	9204	0.941	0.946	96.5558	0.283
3.253-3.353	0.293	393	0.263	8190	0.264	8901	0.941	0.954	96.4274	0.253
3.353-3.463	0.287	403	0.285	7917	0.286	8635	0.948	0.925	96.3521	0.276
3.463-3.584	0.272	408	0.25	7566	0.251	8338	0.949	0.96	95.6344	0.233
3.584-3.72	0.295	369	0.277	7113	0.277	8078	0.846	0.901	92.6219	0.26
3.72-3.871	0.31	355	0.253	7192	0.256	7733	0.917	0.953	97.5947	0.234
3.871-4.043	0.24	360	0.21	6910	0.211	7450	0.962	0.973	97.5839	0.187
4.043-4.24	0.23	373	0.188	6534	0.19	7107	0.967	0.979	97.1859	0.164
4.24-4.468	0.207	319	0.18	6224	0.181	6755	0.974	0.98	96.8616	0.159
4.468-4.738	0.202	310	0.175	5843	0.177	6397	0.974	0.981	96.1857	0.155
4.738-5.064	0.222	283	0.177	5440	0.179	6029	0.97	0.981	94.9245	0.153
5.064-5.469	0.236	279	0.184	5196	0.187	5575	0.968	0.979	98.2063	0.157
5.469-5.988	0.249	215	0.199	4818	0.201	5145	0.963	0.977	97.8231	0.169
5.988-6.69	0.247	231	0.198	4286	0.201	4648	0.971	0.977	97.1816	0.17
6.69-7.717	0.238	189	0.193	3750	0.195	4107	0.966	0.98	95.9094	0.171
7.717-9.431	0.18	162	0.137	3281	0.139	3490	0.978	0.989	98.6533	0.134
9.431-13.251	0.133	165	0.133	2473	0.133	2709	0.989	0.989	97.3791	0.142
13.251-82.792	0.305	73	0.263	1395	0.265	1503	0.935	0.946	97.6713	0.285

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.8554	0.2775	0.4242	2.4799	0.1534	3.2208	0.055	0.2152	-0.225	-0.1239	-0.0161	-0.1068	0.3493	0.1872	-0.0389	0.0913	0.0468	0.0414	0.0629	-0.0027	0.0612	21.1946	-3.1259	15.9318
2	0.6112	-0.0421	-0.3913	0.3697	-0.2123	0.5174	0.0032	0.0116	0.0278	0.0204	0.0373	0.0706	0.0123	-0.0421	-0.0406	0.0978	0.0199	0.0467	0.0983	-0.0385	0.0668	28.5335	9.8912	16.4761
3	2.6689	-0.5456	0.6303	2.201	-0.5943	3.0508	-0.0094	-0.3537	-0.2201	0.2584	0.095	0.1253	0.3509	-0.3529	-0.0856	0.2081	0.0051	0.1023	0.1713	0.0552	0.0978	43.3407	45.7261	29.2236
4	0.4769	0.0243	-0.1698	0.3515	0.4192	0.5862	-0.0183	-0.0221	-0.1028	0.0397	0.0479	-0.0506	0.0468	0.0487	-0.0296	0.1892	0.0825	0.1062	0.1097	0.0744	0.1047	42.5005	60.8156	28.6087
5	3.9931	-0.9307	0.7576	2.2441	0.3336	3.6464	-0.7002	-0.3812	0.6376	0.4884	0.2784	-0.5949	-0.9881	0.082	0.4218	0.9509	-0.0676	-0.0339	0.3794	0.0378	0.519	-2.1304	42.7499	-47.7433
6	0.7616	0.0619	-0.0607	0.8135	-0.207	1.0601	-0.1489	0.3472	0.142	-0.4857	0.0942	-0.1907	-0.1301	0.2055	0.0547	0.4796	-0.1048	0.1655	0.3512	0.0046	0.2489	-12.4677	30.9523	-49.6617
7	3.5721	0.8787	0.4779	1.4747	1.0128	2.482	-0.64	0.8429	1.0028	-0.3744	0.1818	0.3837	-0.952	0.4192	0.4582	1.1557	-0.2507	-0.0102	0.6348	0.0728	0.5575	-12.0018	99.2674	-75.9316
8	0.6286	0.0652	0.0068	0.9777	0.2977	1.0466	0.0523	-0.2825	0.2384	0.4967	-0.0914	0.057	-0.266	-0.1458	0.0391	0.624	0.0316	0.1631	0.3488	-0.0003	0.2333	-7.9656	83.796	-74.0001
9	7.6177	0.9081	-1.2126	0.7071	-1.4953	3.2932	0.1167	-0.1459	-0.4042	0.0662	-0.0458	-0.0401	-0.1253	0.0902	-0.0709	0.0601	0.0241	-0.0032	0.1006	-0.0046	0.2686	70.804	-6.9199	22.9736
10	7.9512	0.6501	-2.4379	7.9877	-1.2125	4.0584	-0.1981	0.181	0.1447	0.1463	0.3679	0.619	-0.2814	-0.4664	-0.1698	0.1431	0.0504	0.019	0.2743	-0.1027	0.1417	-2.9035	64.6636	22.3391
11	0.6897	2.8969	0.7913	13.1284	2.4025	5.9932	0.0129	0.0079	-0.1145	0.1458	0.326	-0.3141	0.4859	0.1878	-0.3388	0.0811	0.0935	-0.0058	0.2172	0.023	0.3559	5.7891	2.0479	-19.1141
12	5.0246	3.0318	-3.4136	4.7798	2.0209	8.0754	0.0996	-0.3315	-0.0133	0.3223	-0.4079	0.2865	0.4184	0.0693	0.3083	0.1691	0.1135	-0.0728	0.4803	0.1064	0.4116	-37.4317	64.9969	-103.78

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