PDB-5bxq: Structure of the NTF2:RanGDP complex

ID or keywords:

Entry

Database: PDB / ID: 5bxq

Title

Structure of the NTF2:RanGDP complex

Components

GTP-binding nuclear protein Ran
Nuclear transport factor 2

Keywords

TRANSPORT PROTEIN / Nuclear transport / RanGDP / NTF2

Function / homology

Function and homology information

negative regulation of vascular endothelial growth factor production / RISC complex binding / protein localization to nuclear pore / pre-miRNA binding / nuclear pore central transport channel / pre-miRNA export from nucleus / snRNA import into nucleus / nuclear export signal receptor activity / structural constituent of nuclear pore / RISC complex ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Canis familiaris (dog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Stewart, M.

Citation

Journal: J.Mol.Biol. / Year: 1998
Title: Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran.
Authors: Stewart, M. / Kent, H.M. / McCoy, A.J.

History

Deposition	Jun 9, 2015	Deposition site: RCSB / Processing site: PDBE
Supersession	Jul 1, 2015	ID: 1A2K
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5bxq.cif.gz	354 KB	Display	PDBx/mmCIF format
PDB format	pdb5bxq.ent.gz	290.3 KB	Display	PDB format
PDBx/mmJSON format	5bxq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5bxq_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5bxq_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5bxq_validation.xml.gz	34.1 KB	Display
Data in CIF	5bxq_validation.cif.gz	47.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bx/5bxq ftp://data.pdbj.org/pub/pdb/validation_reports/bx/5bxq	HTTPS FTP

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Related structure data

Similar structure data	1a2k-d 5ck5-d 1xfu-6 6p4w-1 1xfu-3 4cfs-d 1xfu-2 1xfw-1 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 (3) #205 - Jan 2017 Nuclear Pore Complex similarity (2) #44 - Aug 2003 Calmodulin similarity (1)

Deposited unit

A: Nuclear transport factor 2

B: Nuclear transport factor 2

C: GTP-binding nuclear protein Ran

D: GTP-binding nuclear protein Ran

E: GTP-binding nuclear protein Ran

hetero molecules

104 kDa, 5 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)	155.116, 120.439, 108.836
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

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Protein , 2 types, 5 molecules ABCDE

#1: Protein	Nuclear transport factor 2 / NTF-2 Mass: 14491.425 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nutf2, Ntf2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61972
#2: Protein	GTP-binding nuclear protein Ran / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein Mass: 24456.105 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis familiaris (dog) / Gene: RAN / Production host: Escherichia coli (E. coli) / References: UniProt: P62825

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Non-polymers , 4 types, 350 molecules

#3: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Li2SO4, 50 mM Na Citrate pH5.6, 15% PEG4000 / PH range: 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.88 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 1996
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.88 Å / Relative weight: 1
Reflection	Resolution: 2.5→100 Å / Num. obs: 35633 / % possible obs: 99.9 % / Redundancy: 5.4 % / B_iso Wilson estimate: 33.75 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 7.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→24.946 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2249	1791	5.08 %
R_work	0.1835	-	-
obs	0.1856	35228	99.06 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→24.946 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6732	0	92	343	7167

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7002
X-RAY DIFFRACTION	f_angle_d	0.812	9515
X-RAY DIFFRACTION	f_dihedral_angle_d	14.574	2549
X-RAY DIFFRACTION	f_chiral_restr	0.03	1039
X-RAY DIFFRACTION	f_plane_restr	0.003	1207

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5-2.5676	0.331	152	0.2803	2529	X-RAY DIFFRACTION	99
2.5676-2.643	0.2782	142	0.2508	2538	X-RAY DIFFRACTION	99
2.643-2.7282	0.3065	149	0.2441	2545	X-RAY DIFFRACTION	99
2.7282-2.8256	0.2757	139	0.237	2513	X-RAY DIFFRACTION	99
2.8256-2.9386	0.273	128	0.2147	2561	X-RAY DIFFRACTION	99
2.9386-3.0721	0.2779	134	0.2214	2564	X-RAY DIFFRACTION	99
3.0721-3.2338	0.2851	133	0.2185	2509	X-RAY DIFFRACTION	98
3.2338-3.4359	0.2298	123	0.1902	2555	X-RAY DIFFRACTION	99
3.4359-3.7004	0.2414	126	0.1799	2583	X-RAY DIFFRACTION	99
3.7004-4.0713	0.2077	132	0.1591	2592	X-RAY DIFFRACTION	99
4.0713-4.6571	0.1823	149	0.1302	2576	X-RAY DIFFRACTION	99
4.6571-5.8549	0.1593	145	0.1449	2628	X-RAY DIFFRACTION	100
5.8549-24.947	0.1757	139	0.1643	2744	X-RAY DIFFRACTION	100

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	0.0845	0.0222	-0.025	0.1319	-0.1673	0.2041	-0.0619	0.1288	0.0804	-0.1449	0.2631	-0.2055	0.1279	0.197	-0	0.3237	0.0057	-0.0485	0.3072	0.0352	0.24	25.714	15.8183	73.3148
2	0.0857	0.0575	0.0432	0.1692	0.0799	0.042	0.0361	-0.265	0.1308	-0.0513	0.0811	0.3671	0.1005	-0.276	0.0001	0.3113	0.0237	0.0128	0.303	0.0261	0.3591	18.253	19.6178	86.8614
3	0.0306	-0.0485	0.0088	0.0744	0.0111	0.0616	0.0083	0.2227	0.4677	0.0989	0.1762	0.1795	-0.415	-0.2743	0	0.3127	0.0552	-0.0257	0.376	-0.0041	0.3088	22.6535	26.4888	89.0241
4	0.2072	-0.3152	-0.0791	0.4377	0.1476	0.3392	0.1114	-0.0558	0.0059	-0.0274	-0.1101	-0.0155	-0.0722	-0.0918	0	0.219	-0.0182	-0.0377	0.2525	0.027	0.224	28.2557	13.0436	81.1689
5	0.0726	-0.1969	-0.1554	0.2448	0.3268	0.2646	-0.0951	-0.0673	-0.2982	0.1611	0.1534	0.0698	-0.1112	-0.2284	-0.0004	0.2293	-0.047	-0.0249	0.2218	0.0357	0.254	24.5657	12.2614	86.1092
6	0.0997	0.0795	-0.0475	0.079	-0.0806	0.1062	0.0866	-0.5575	0.0774	-0.0932	0.1626	0.0147	-0.1161	0.1256	0	0.3723	-0.0402	0.0449	0.3701	0.1032	0.3907	23.3192	-3.8924	94.8883
7	0.015	0.2095	-0.1194	0.7066	0.0089	0.4194	-0.0506	-0.0908	-0.2031	-0.0317	0.0889	0.1252	0.1232	0.0433	0	0.2728	-0.0239	0.0123	0.2533	0.0152	0.3348	28.8702	-5.8289	84.2306
8	0.1507	0.1758	-0.1037	0.1335	-0.1009	0.1128	-0.1262	-0.021	0.1836	0.0982	-0.0563	0.0697	-0.0856	0.0847	-0.0001	0.2796	-0.0041	0.0046	0.4142	0.0372	0.2708	36.5772	0.5136	91.4709
9	0.1091	-0.1923	-0.1112	0.3113	0.1395	-0.0974	-0.1056	-0.1274	-0.0406	-0.1817	0.0085	0.0707	0.106	-0.076	0	0.2453	-0.0525	-0.0068	0.2871	0.0473	0.2531	27.2217	0.576	84.7135
10	-0.0097	-0.0117	0.0123	0.057	0.0112	0.136	0.0236	-0.1015	0.0375	-0.0564	0.0461	0.2103	-0.0554	0.0204	-0	0.2269	-0.0093	0.0394	0.2109	0.035	0.2159	59.2452	1.573	79.2349
11	0.0064	-0.027	-0.0148	0.0736	-0.0865	0.1008	-0.0761	-0.3441	0.1936	0.1257	0.05	-0.0617	-0.0966	0.08	-0	0.2921	-0.0216	0.0069	0.3598	-0.0526	0.2693	58.7642	7.1145	88.2867
12	0.0304	0.0803	-0.009	0.3415	-0.0216	0.4501	-0.0234	0.0128	0.0371	0.0585	-0.0581	-0.0107	0.0304	0.0161	-0	0.2245	-0.0023	0.0003	0.2185	-0.0096	0.2296	57.3738	5.0097	77.8349
13	0.1824	-0.0173	0.1623	0.095	-0.014	0.1732	-0.0881	0.1769	-0.1873	-0.1765	0.1775	0.2937	0.0542	-0.2166	0	0.3362	-0.0282	0.0057	0.2725	0.0069	0.3081	51.6338	-3.4573	69.0932
14	0.1152	0.0471	0.0456	0.0793	0.1125	0.1073	-0.4393	0.564	-0.3125	-0.356	0.1062	0.1914	0.1686	0.1477	-0.0002	0.5552	0.0189	0.0801	0.4104	-0.0136	0.4396	60.0546	-16.5414	70.8351
15	0.1197	0.0503	-0.0248	0.0222	-0.1373	0.1404	0.123	-0.2055	-0.183	0.0324	-0.0216	-0.0162	0.2132	0.2613	0.0028	0.2769	0.0324	0.0612	0.2526	0.0113	0.3095	65.9875	-7.3605	74.4682
16	0.0822	0.0264	0.0247	0.0084	0.0058	0.0019	-0.1488	0.3279	0.043	-0.3032	-0.0038	-0.1278	0.2731	0.1008	0.0001	0.3212	-0.0273	-0.003	0.3361	-0.0044	0.3081	67.624	3.7736	68.6953
17	0.1024	0.1412	0.0556	0.099	0.047	0.0155	0.0739	-0.1295	-0.2104	-0.0754	-0.1193	-0.436	0.084	0.0443	-0.0075	0.322	0.0319	-0.0025	0.4061	-0.0135	0.2629	75.6373	5.1333	70.1712
18	0.0292	-0.0005	-0.0694	0.0353	-0.0167	0.0422	-0.0303	-0.3178	0.0043	0.2206	-0.0167	-0.4008	0.2921	0.2938	-0.0001	0.375	0.0546	0.0131	0.3034	0.0291	0.2492	70.2383	-10.1545	84.4929
19	0.0484	-0.0294	-0.0518	0.014	0.0046	0.0282	0.4947	0.0714	-0.2874	-0.1143	0.2656	0.0844	0.1736	0.3378	0.0005	0.6625	0.0602	0.0157	0.5438	-0.0292	0.6005	70.2995	-16.5982	67.2771
20	0.1085	0.104	-0.0595	0.0584	-0.0769	0.0667	0.219	0.0329	0.0526	-0.2954	-0.3196	0.0478	0.1009	0.108	-0.0119	0.261	0.0256	0.0486	0.2359	-0.0143	0.2397	44.6801	25.7463	105.5675
21	0.0474	0.1317	-0.0365	0.196	-0.0495	-0.0035	-0.0578	-0.0698	0.004	-0.0316	-0.0195	0.0345	0.0157	-0.0436	0	0.2776	-0.0041	0.019	0.2579	-0.0188	0.2431	51.2017	23.1882	104.5588
22	0.1786	-0.3381	0.0312	0.2473	-0.0331	0.2623	0.0133	-0.125	0.0753	0.0772	-0.1649	0.2517	0.1094	-0.3195	-0.0032	0.2772	-0.0538	0.033	0.276	-0.0399	0.3091	33.9853	23.8559	107.9764
23	1.127	0.0684	-0.0856	0.1875	0.0694	0.0563	0.0512	0.0909	0.6472	0.126	-0.2122	-0.0316	-0.2397	-0.2283	-0.0325	0.328	0.0871	0.0439	0.3322	-0.0888	0.4323	32.1566	41.0163	111.1999
24	0.0583	-0.0283	0.0326	0.1191	0.0663	0.0534	-0.0379	-0.0331	0.0573	-0.0024	-0.0481	-0.1247	-0.0015	-0.3066	0	0.2942	-0.0293	0.0356	0.3129	-0.0559	0.3438	43.0048	37.1453	111.0472
25	0.1279	0.1168	-0.0973	0.2411	0.2059	0.158	0.049	-0.1304	0.2356	0.0996	0.0719	-0.0291	-0.1283	-0.1668	0	0.2755	0.0125	0.0194	0.2929	-0.0111	0.2719	49.9696	33.5397	114.4256
26	0.5593	0.734	0.5725	1.035	0.8821	0.978	-0.2148	-0.595	0.4388	0.1232	0.7931	-0.0318	-0.3443	0.2603	-0.0443	0.417	0.2205	0.0044	0.5351	-0.1925	0.4366	36.8109	45.7835	119.0324
27	0.4095	-0.045	-0.3321	0.5222	-0.0308	0.4103	0.0262	-0.0324	0.0504	-0.0534	0.0176	-0.0811	0.0832	0.1623	0	0.2361	0.0044	0.0079	0.3084	-0.0251	0.2181	1.2611	-33.5097	102.743
28	0.1186	-0.2097	0.0532	0.3065	-0.0918	0.0395	0.0683	-0.1496	0.1439	-0.1442	0.1498	-0.4567	-0.2096	-0.027	0.0002	0.3586	-0.0899	0.0374	0.365	-0.0746	0.4465	8.226	-17.6047	105.0838
29	0.3345	-0.0412	-0.0565	-0.0471	-0.1204	0.1363	0.0849	0.0104	0.257	0.0287	0.0053	-0.0407	-0.0244	0.0564	0	0.2699	-0.0377	0.0608	0.2214	0.0011	0.3137	-2.0997	-17.5123	102.5145

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 63 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 127 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 24 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 80 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 81 through 96 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 97 through 127 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 8 through 29 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 30 through 44 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 45 through 91 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 92 through 122 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 123 through 143 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 144 through 158 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 159 through 169 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 170 through 179 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 180 through 190 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 191 through 204 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 7 through 29 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 30 through 66 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 67 through 122 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 123 through 143 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 144 through 158 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 159 through 190 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 191 through 208 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 8 through 122 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 123 through 148 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 149 through 212 )

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