PDB-3w3z: Crystal structure of Kap121p bound to RanGTP

ID or keywords:

Entry

Database: PDB / ID: 3w3z

Title

Crystal structure of Kap121p bound to RanGTP

Components

GTP-binding nuclear protein Ran
Importin subunit beta-3

Keywords

PROTEIN TRANSPORT/NUCLEAR PROTEIN / HEAT repeat / nuclear import / PROTEIN TRANSPORT-NUCLEAR PROTEIN complex

Function / homology

Function and homology information

regulation of protein desumoylation / RISC complex binding / pre-miRNA binding / pre-miRNA export from nucleus / snRNA import into nucleus / nuclear export signal receptor activity / nuclear localization sequence binding / RISC complex / GTP metabolic process / nuclear import signal receptor activity ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Canis lupus familiaris (dog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.7 Å

Authors

Kobayashi, J. / Matsuura, Y.

Citation

Journal: J.Mol.Biol. / Year: 2013
Title: Structural basis for cell-cycle-dependent nuclear import mediated by the karyopherin Kap121p.
Authors: Kobayashi, J. / Matsuura, Y.

History

Deposition	Dec 28, 2012	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 10, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2014	Group: Database references
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3w3z.cif.gz	479.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3w3z.ent.gz	392.8 KB	Display	PDB format
PDBx/mmJSON format	3w3z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3w3z_validation.pdf.gz	746 KB	Display	wwPDB validaton report
Full document	3w3z_full_validation.pdf.gz	783.1 KB	Display
Data in XML	3w3z_validation.xml.gz	49.1 KB	Display
Data in CIF	3w3z_validation.cif.gz	64 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w3/3w3z ftp://data.pdbj.org/pub/pdb/validation_reports/w3/3w3z	HTTPS FTP

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Related structure data

Related structure data	3w3tC 3w3uC 3w3vC 3w3wC 3w3xC 3w3yC C: citing same article (ref.)
Similar structure data	5d2n-1 6t9w-d 11786 4r1m-d 2x6g-d 2qza-d 2eac-d 3dlh-d Search similar-shape structures by Omokage search (details) 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 (4) #205 - Jan 2017 Nuclear Pore Complex similarity (2)

Deposited unit

A: Importin subunit beta-3

B: GTP-binding nuclear protein Ran

hetero molecules

143 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	97.750, 97.750, 289.981
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Importin subunit beta-3 / Karyopherin subunit beta-3 / Karyopherin-121 / Protein secretion enhancer 1 Mass: 122304.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P32337
#2: Protein	GTP-binding nuclear protein Ran / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein Mass: 20210.416 Da / Num. of mol.: 1 / Fragment: UNP residues 1-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: RAN / Production host: Escherichia coli (E. coli) / References: UniProt: P62825
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.81 Å³/Da / Density % sol: 56.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES, 0.2M CaCl2, 10% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97897 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 14, 2010
Radiation	Monochromator: rotated inclined double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97897 Å / Relative weight: 1
Reflection	Resolution: 2.7→48.77 Å / Num. all: 45236 / Num. obs: 45100 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.7→2.79 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
BSS		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
MOSFLM		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.7→46.36 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.889 / SU B: 32.352 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.869 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29778	2223	4.9 %	RANDOM
R_work	0.26056	-	-	-
all	0.2624	45236	-	-
obs	0.2624	42804	99.65 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 99.485 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.08 Å²	2.08 Å²	0 Å²
2-	-	2.08 Å²	0 Å²
3-	-	-	-6.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→46.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9109	0	33	4	9146

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	9310
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	8960
X-RAY DIFFRACTION	r_angle_refined_deg	1.627	1.981	12672
X-RAY DIFFRACTION	r_angle_other_deg	0.887	3	20554
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.705	5	1169
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.894	24.973	376
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.433	15	1488
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.436	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	1522
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	10397
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2016
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.364	145	-
R_work	0.349	3142	-
obs	-	-	99.94 %

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	0.8136	0.5346	0.1471	1.2719	0.3108	0.9603	-0.0343	-0.1558	0.1175	-0.3527	-0.1912	0.0094	0.1792	0.6525	0.2255	0.196	0.2548	0.0703	0.6776	-0.0222	0.4687	-10.8054	16.1747	-23.6552
2	1.6234	0.9292	-1.2996	0.9922	-1.9593	4.3157	0.4273	-0.4538	-0.2091	0.2882	-0.5601	-0.0344	-0.4908	1.1226	0.1328	0.1093	-0.1245	-0.0709	0.8399	-0.0597	0.5807	-6.72	25.8225	2.3733
3	0.6826	0.337	0.0318	0.1959	-0.2279	4.0508	0.5539	-0.0988	-0.1437	0.3247	-0.1562	0.0319	-1.1911	1.546	-0.3977	0.8034	-0.4791	-0.0404	0.8336	-0.2482	0.5093	-17.7034	24.8892	14.4681
4	7.6452	1.1812	2.1186	2.3552	-1.0194	1.4633	0.3936	-0.3994	0.1186	1.4002	-0.2182	0.4895	-0.7771	0.1764	-0.1754	0.8885	-0.1811	0.2288	0.6574	-0.2861	0.3519	-28.8074	20.4103	20.6143
5	2.7974	-1.243	0.3163	0.5871	-0.3829	5.3772	0.3968	0.1824	-0.4475	-0.0754	-0.17	0.225	-0.9694	0.8889	-0.2268	0.368	-0.1909	-0.032	0.6056	-0.0944	0.4535	-23.627	15.0949	21.0761
6	1.9712	2.0584	0.1603	3.3349	-0.4544	0.3716	0.6903	-0.281	-0.1446	0.9072	-0.4767	0.3257	-0.192	0.1828	-0.2136	0.6548	-0.1794	0.1463	0.6476	-0.1612	0.2287	-32.1926	12.6975	32.2984
7	0.9733	1.394	0.1778	2.1114	0.4187	0.4883	0.1546	-0.1619	-0.0336	0.153	-0.0973	0.0751	-0.1895	0.0053	-0.0573	0.1715	0.1234	0.0975	0.5506	0.0664	0.5296	-48.9043	-10.9154	24.9993
8	0.1801	-0.0109	-0.3183	0.317	-0.8095	2.7439	0.1526	0.0239	-0.0421	-0.1314	-0.0326	0.1045	0.0913	0.1154	-0.12	0.1723	0.104	-0.0192	0.3528	-0.0265	0.6299	-26.9115	-39.5496	11.694
9	0.1651	-0.1686	0.5123	0.273	-0.884	3.5809	0.0188	0.0059	-0.0953	0.0212	-0.1905	-0.0191	0.062	0.5598	0.1717	0.1245	0.0462	-0.048	0.635	0.1382	0.5343	-15.964	-51.5917	43.7652
10	2.8784	0.1341	-1.8703	4.0501	-6.7145	12.7233	-0.6102	-0.3315	-0.6877	0.1156	-0.0484	-0.199	-0.3932	-0.51	0.6587	0.545	0.25	0.0212	0.8498	0.0382	0.3615	-35.9036	-50.9924	54.4116
11	13.0351	18.0073	10.974	29.8253	17.625	10.6921	0.3813	-0.6351	-0.0042	1.8979	-0.1403	0.1895	0.7313	-0.2573	-0.241	0.7172	0.2604	0.4254	0.6346	0.1635	0.4133	-37.6892	-49.4192	69.9032
12	7.1195	-9.145	-5.5467	13.2414	8.6386	5.8556	0.2058	-0.9485	-0.8866	-1.0522	0.2873	-0.0225	-0.9567	-0.208	-0.4932	0.45	0.5747	0.5158	1.2941	0.5812	1.1148	-37.057	-38.5185	59.3037
13	2.0786	-1.7577	-0.6115	3.0975	0.7448	0.2181	0.1715	0.0386	0.0769	-0.1404	-0.1859	0.1211	-0.012	0.0083	0.0144	0.2741	0.2771	-0.1197	0.3204	-0.0568	0.6052	-32.7069	6.8502	-11.2219
14	5.6437	3.4702	5.797	27.0967	1.9957	6.0537	0.0479	0.1734	0.2453	0.1799	-0.278	0.6388	0.0167	0.2015	0.2301	0.3325	0.0576	-0.0609	0.3506	-0.0375	0.4082	-39.8743	-1.7751	-9.4845
15	7.062	9.3302	4.9494	12.417	6.8084	13.4682	0.4213	-0.0968	-1.0431	0.7159	-0.432	-1.1763	0.7824	-0.6422	0.0107	0.4248	0.1847	0.0133	0.3097	-0.2619	0.7076	-33.0087	-10.7093	-9.1591
16	14.922	-7.5752	-0.2298	9.7075	-1.3689	0.3804	0.0036	0.409	-0.5526	-0.4956	0.0308	0.4226	0.1252	-0.0564	-0.0344	0.3707	0.1096	-0.0079	0.3977	-0.0891	0.409	-28.8232	0.2092	-17.8596
17	0.3451	-0.7749	-0.399	1.9457	0.5595	1.03	0.0505	-0.0446	-0.0425	-0.1406	-0.0505	0.1287	-0.0205	0.2632	0	0.2338	0.2285	-0.0725	0.3212	-0.046	0.5793	-30.1867	7.4016	-11.6997
18	1.0678	0.1582	-0.0616	3.1898	-3.227	3.3798	-0.1182	-0.1427	-0.1574	-0.1222	-0.0734	-0.2372	0.1282	0.319	0.1916	0.3459	0.216	-0.0353	0.5134	-0.0898	0.4891	-21.5872	6.3116	-2.5588
19	21.3151	7.2718	10.4419	13.1512	-9.3935	20.89	0.453	0.6683	-1.5968	1.624	-0.0843	-1.1165	-1.1797	0.3277	-0.3687	0.9443	-0.0722	-0.2581	0.6508	0.0307	0.3454	-25.1898	-6.2364	9.4581
20	0.0108	-0.3002	-0.1158	17.8016	7.4201	3.1097	0.3302	0.0486	0.0577	1.7386	-0.5307	-0.5794	0.7291	-0.3183	0.2005	0.3713	0.1884	-0.1405	0.7649	0.1122	0.6203	-21.5506	7.7086	9.0902
21	0.4773	0.9378	-0.1805	3.1093	-0.2168	0.7535	-0.1565	-0.2421	-0.042	-0.1538	0.093	0.1723	0.0341	0.3647	0.0635	0.2361	0.2218	-0.0496	0.4658	-0.0053	0.5829	-34.1618	7.6533	0.8236
22	13.7554	3.9203	-0.9674	6.75	-0.0813	2.151	0.0986	-0.0633	0.0955	0.2413	-0.0224	0.0285	-0.175	-0.0623	-0.0762	0.2044	0.1593	-0.0443	0.3039	-0.0722	0.5099	-40.4097	18.9305	-2.8311

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 167
2	X-RAY DIFFRACTION	2	A	168 - 259
3	X-RAY DIFFRACTION	3	A	260 - 298
4	X-RAY DIFFRACTION	4	A	299 - 337
5	X-RAY DIFFRACTION	5	A	338 - 370
6	X-RAY DIFFRACTION	6	A	371 - 450
7	X-RAY DIFFRACTION	7	A	451 - 623
8	X-RAY DIFFRACTION	8	A	624 - 865
9	X-RAY DIFFRACTION	9	A	866 - 1044
10	X-RAY DIFFRACTION	10	A	1045 - 1062
11	X-RAY DIFFRACTION	11	A	1063 - 1071
12	X-RAY DIFFRACTION	12	A	1072 - 1088
13	X-RAY DIFFRACTION	13	B	6 - 27
14	X-RAY DIFFRACTION	14	B	28 - 33
15	X-RAY DIFFRACTION	15	B	34 - 41
16	X-RAY DIFFRACTION	16	B	42 - 48
17	X-RAY DIFFRACTION	17	B	49 - 92
18	X-RAY DIFFRACTION	18	B	93 - 126
19	X-RAY DIFFRACTION	19	B	127 - 131
20	X-RAY DIFFRACTION	20	B	132 - 141
21	X-RAY DIFFRACTION	21	B	142 - 166
22	X-RAY DIFFRACTION	22	B	167 - 176

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