PDB-8hkw: Crystal structure of importin-alpha3 bound to the 53BP1 nuclear l...

ID or keywords:

Entry

Database: PDB / ID: 8hkw

Title

Crystal structure of importin-alpha3 bound to the 53BP1 nuclear localization signal

Components

Importin subunit alpha-3
Peptide from TP53-binding protein 1

Keywords

TRANSPORT PROTEIN / importin alpha / nuclear localization signal / nuclear import

Function / homology

Function and homology information

ubiquitin-modified histone reader activity / positive regulation of isotype switching / dopamine secretion / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / NS1 Mediated Effects on Host Pathways / protein localization to site of double-strand break / NLS-dependent protein nuclear import complex / DNA repair complex / nuclear import signal receptor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Matsuura, Y.

Funding support

Japan, 1items

Citation

Journal: Data Brief / Year: 2023
Title: Crystallographic data of an importin-alpha 3 dimer in which the two protomers are bridged by a bipartite nuclear localization signal.
Authors: Matsuura, Y.

History

Deposition	Nov 28, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 21, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 15, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	8hkw_validation.pdf.gz	447.2 KB	Display	wwPDB validaton report
Full document	8hkw_full_validation.pdf.gz	453.8 KB	Display
Data in XML	8hkw_validation.xml.gz	35.3 KB	Display
Data in CIF	8hkw_validation.cif.gz	51.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hk/8hkw ftp://data.pdbj.org/pub/pdb/validation_reports/hk/8hkw	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 (12) #205 - Jan 2017 Nuclear Pore Complex similarity (3) #99 - Mar 2008 Cadherin similarity (4) #55 - Jul 2004 DNA Ligase similarity (5) #88 - Apr 2007 Clathrin similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (1) #150 - Jun 2012 Sliding Clamps similarity (4) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#85 - Jan 2007
Importins
similarity (12)
#205 - Jan 2017
Nuclear Pore Complex
similarity (3)
#99 - Mar 2008
Cadherin
similarity (4)
#55 - Jul 2004
DNA Ligase
similarity (5)
#88 - Apr 2007
Clathrin
similarity (2)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (4)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Importin subunit alpha-3

B: Importin subunit alpha-3

C: Peptide from TP53-binding protein 1

D: Peptide from TP53-binding protein 1

96.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	95.703, 79.600, 117.440
Angle α, β, γ (deg.)	90.00, 95.57, 90.00
Int Tables number	5
Space group name H-M	I121

#1: Protein	Importin subunit alpha-3 / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4 Mass: 45761.113 Da / Num. of mol.: 2 / Fragment: UNP residues 70-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00629
#2: Protein/peptide	Peptide from TP53-binding protein 1 / p53BP1 Mass: 2508.878 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Mother liquor contained PEG3350 and lithium nitrate. Crystal was grown in the presence of a synthetic peptide (amino acid sequence: GTSFSGRKIKTAVRRRK) that corresponds to human Nup153 residues 1459-1475).

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Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.9→27.34 Å / Num. obs: 68772 / % possible obs: 99.4 % / Redundancy: 3 % / B_iso Wilson estimate: 25.9 Å² / CC_1/2: 0.993 / Net I/σ(I): 4.9
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4433 / CC_1/2: 0.338 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	v1.14	refinement
MOSFLM		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→27.338 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2214	3548	5.17 %
R_work	0.2006	-	-
obs	0.2017	68669	99.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→27.338 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6750	0	0	502	7252

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6892
X-RAY DIFFRACTION	f_angle_d	0.535	9402
X-RAY DIFFRACTION	f_dihedral_angle_d	14.325	4222
X-RAY DIFFRACTION	f_chiral_restr	0.038	1128
X-RAY DIFFRACTION	f_plane_restr	0.004	1224

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 (%)
1.9-1.926	0.4037	142	0.3787	2561	X-RAY DIFFRACTION	98
1.926-1.9535	0.3811	125	0.36	2613	X-RAY DIFFRACTION	99
1.9535-1.9827	0.3806	149	0.3461	2548	X-RAY DIFFRACTION	99
1.9827-2.0137	0.3676	140	0.3123	2626	X-RAY DIFFRACTION	99
2.0137-2.0467	0.3024	140	0.297	2568	X-RAY DIFFRACTION	99
2.0467-2.0819	0.3072	154	0.2727	2610	X-RAY DIFFRACTION	99
2.0819-2.1198	0.3347	148	0.2639	2595	X-RAY DIFFRACTION	100
2.1198-2.1605	0.3007	149	0.258	2593	X-RAY DIFFRACTION	99
2.1605-2.2046	0.2825	127	0.238	2597	X-RAY DIFFRACTION	99
2.2046-2.2525	0.2566	139	0.2402	2562	X-RAY DIFFRACTION	99
2.2525-2.3049	0.2389	144	0.2208	2587	X-RAY DIFFRACTION	98
2.3049-2.3625	0.2698	151	0.2254	2571	X-RAY DIFFRACTION	98
2.3625-2.4264	0.212	143	0.205	2565	X-RAY DIFFRACTION	99
2.4264-2.4977	0.2378	160	0.2071	2641	X-RAY DIFFRACTION	100
2.4977-2.5783	0.2698	141	0.2087	2606	X-RAY DIFFRACTION	100
2.5783-2.6703	0.2424	128	0.2158	2623	X-RAY DIFFRACTION	100
2.6703-2.7772	0.2322	136	0.2073	2618	X-RAY DIFFRACTION	100
2.7772-2.9034	0.2479	137	0.21	2631	X-RAY DIFFRACTION	100
2.9034-3.0563	0.2344	138	0.2066	2632	X-RAY DIFFRACTION	100
3.0563-3.2475	0.2127	145	0.2015	2569	X-RAY DIFFRACTION	99
3.2475-3.4978	0.234	147	0.2108	2575	X-RAY DIFFRACTION	98
3.4978-3.8489	0.1775	135	0.1703	2644	X-RAY DIFFRACTION	100
3.8489-4.4039	0.1615	141	0.1532	2650	X-RAY DIFFRACTION	100
4.4039-5.5408	0.1775	149	0.1634	2660	X-RAY DIFFRACTION	100
5.5408-27.338	0.1637	140	0.1589	2676	X-RAY DIFFRACTION	99

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	0.0787	-0.0589	-0.114	0.0927	0.1241	0.1521	-0.236	0.5059	0.279	-0.8451	0.1085	0.3634	-0.1546	0.0751	-0.0001	0.4608	-0.0138	-0.0456	0.3167	0.0575	0.3359	20.0201	-67.2669	-48.9644
2	0.2265	-0.005	-0.102	0.1378	-0.1089	0.1613	-0.0619	-0.0309	0.2709	0.2351	-0.12	-0.1052	0.1072	0.1595	-0	0.3384	-0.0297	-0.1018	0.3256	0.0115	0.4466	16.4214	-61.681	-36.9599
3	1.8423	-0.6222	-0.1024	0.9928	0.0491	0.958	0.0185	0.0261	0.0532	-0.0848	-0.0626	-0.0308	0.0537	0.0398	0	0.2609	-0.028	-0.0004	0.2257	0.0357	0.2736	4.983	-57.9965	-43.0969
4	0.5074	-0.209	0.1163	0.1054	-0.0007	0.466	-0.0266	-0.0429	-0.0501	0.0126	-0.0033	0.0247	-0.0584	-0.0624	-0	0.2861	-0.0314	0.0008	0.2579	0.0403	0.3215	-7.6134	-54.9973	-34.3898
5	0.1138	-0.1449	-0.0489	0.1662	0.0281	0.2462	-0.0664	0.144	0.4105	-0.3925	-0.1931	0.897	-0.1836	-0.4975	-0.0004	0.3622	-0.0398	-0.0245	0.3154	-0.0354	0.4071	-13.4146	-43.0383	-37.793
6	0.4207	0.3125	-0.532	1.1497	0.9226	1.1713	-0.045	0.047	-0.1447	0.0173	-0.035	0.029	-0.023	-0.046	-0	0.2052	-0.0223	-0.0158	0.2401	0.011	0.2227	-15.3938	-43.2827	-20.4986
7	0.0465	0.0537	-0.0075	0.0218	-0.0309	0.0187	-0.5888	-0.1927	-0.4114	-0.3493	0.2362	-0.476	0.3058	0.7559	0.0001	0.3566	0.0536	0.0056	0.4528	-0.0008	0.4055	-4.4172	-36.7408	-8.962
8	0.3245	0.0714	0.812	0.5926	-0.0882	0.8072	-0.073	-0.2419	0.0281	0.0066	0.0284	-0.0187	-0.2454	-0.1034	-0	0.2945	-0.0063	-0.0057	0.345	-0.0045	0.256	-15.4477	-24.7072	-8.8882
9	0.2722	0.095	0.1395	0.5185	-0.1614	0.2299	-0.4421	0.0377	0.5408	0.022	0.0569	-0.3179	-0.5266	0.106	-0	0.4923	-0.0377	-0.164	0.318	-0.004	0.4491	-7.6559	-14.2713	-9.8774
10	1.6181	-0.3176	0.2766	0.6211	0.2524	0.5085	-0.0632	1.7993	2.1834	-0.1911	-0.8557	-0.6424	-1.6362	-0.1071	0.013	1.059	-0.3044	-0.5781	-0.274	-0.4815	0.6136	-7.9528	-4.9673	-8.7834
11	0.4405	0.1113	-0.0829	0.1287	-0.0537	0.1675	-0.1993	-0.1504	0.1224	-0.2109	-0.1382	-0.0588	0.0125	0.0041	-0.0008	0.2762	0.0362	0.0239	0.3432	-0.0147	0.389	-12.3862	-7.8727	-43.8403
12	0.9474	-1.0017	-0.012	1.1606	0.6106	0.6771	-0.0514	-0.0421	-0.0283	-0.1511	-0.0353	0.0829	-0.0726	-0.1427	-0	0.2919	-0.0191	-0.0032	0.2824	0.0066	0.2921	-4.815	-13.1977	-43.2795
13	1.0828	-0.7745	0.0966	0.8184	-0.225	0.9493	-0.0504	0.0395	-0.1158	-0.0929	0.0695	0.0263	0.0332	-0.0564	0	0.2395	-0.0119	0.0042	0.2028	-0.008	0.2695	7.4245	-18.6483	-41.8407
14	0.6284	0.0794	-0.6441	0.4407	-0.1154	0.6588	-0.1898	-0.2354	0.0453	-0.2262	0.1163	0.1763	0.0277	0.1463	-0	0.264	0.017	-0.0209	0.2318	-0.0221	0.3019	13.6964	-21.9587	-32.4165
15	0.0912	0.1009	0.2244	0.5834	-0.3327	0.3869	-0.0554	0.0251	0.0372	0.1797	0.033	-0.1037	0.0499	0.0434	0	0.2875	0.0161	-0.0238	0.3193	0.0069	0.3718	18.2621	-23.1832	-25.68
16	1.1507	0.0553	0.7781	2.0381	-0.4195	0.8877	-0.0789	-0.1746	0.1154	0.1016	0.009	-0.0047	-0.0443	-0.1221	-0.0001	0.2709	0.0351	0.0412	0.3374	-0.0388	0.2226	21.2779	-36.115	-17.0041
17	0.2307	-0.344	-0.2633	1.3513	-0.1707	0.4412	-0.0964	-0.2592	-0.1803	0.488	0.1669	0.2541	0.1835	-0.2431	0.0294	0.3544	-0.0182	0.1023	0.4088	0.0572	0.2608	17.4722	-51.7615	-6.9253
18	0.1176	0.0609	-0.0424	0.1285	0.0846	0.0534	0.094	0.3161	-0.3204	-0.2484	-0.0504	0.2095	0.5807	-0.1822	0.0002	0.5082	-0.055	0.0584	0.4656	0.1405	0.5329	17.9115	-61.8832	-12.1944
19	0.0898	-0.0528	-0.1809	0.6974	0.1882	0.2474	-0.116	-0.5182	-1.2275	0.1279	0.0569	0.7792	0.7594	-0.2806	0.0002	0.8823	-0.1839	0.1641	0.7078	0.264	0.9804	11.3144	-67.5006	-8.1409
20	0.0155	-0.0026	0.0093	0.0107	0.0064	-0.0028	0.1163	0.4022	-0.1742	-0.0372	0.1027	-0.0312	0.7048	0.1837	0	0.9981	-0.0979	0.0689	0.5493	0.0042	1.0078	15.585	-72.3106	-11.7008
21	0.3004	0.0969	0.126	0.0563	-0.0006	0.0703	0.1898	-0.0701	-0.3996	0.2479	0.2655	-0.3383	-0.3224	0.4635	0.0086	0.3768	-0.0533	0.1188	0.3765	-0.0251	0.2856	-11.2004	-27.7994	-22.341
22	0.0316	0.0127	0.0051	0.0322	0.0024	0.0035	0.0702	-0.062	-0.2635	0.1749	0.0426	0.5188	0.2404	0.149	-0.0001	0.7461	-0.1331	0.0716	0.932	0.0928	0.6878	1.3662	-30.636	-23.6239
23	0.0294	0.1281	0.0519	0.1252	0.0252	0.0136	0.0329	-0.2786	-0.5798	0.1639	0.1448	0.2135	-0.1116	-0.1999	-0	0.3824	0.0427	0.0218	0.4344	0.0503	0.3779	0.5333	-20.8435	-29.2926
24	0.093	0.0356	0.0123	0.0366	0.0487	0.0326	0.0646	-0.1722	0.6492	0.1275	0.2996	0.7374	0.4458	-0.4997	0.0012	0.3464	-0.0447	-0.0676	0.3772	0.0309	0.4633	16.8505	-45.7863	-22.353
25	0.0083	0.0111	-0.0039	0.0343	0.0055	0.0104	0.0459	0.0962	0.1044	0.461	0.3583	-0.6017	-0.0103	0.4677	-0.0003	0.5975	-0.0948	-0.0037	0.7488	0.0356	0.9529	2.9418	-43.6871	-23.7853
26	0.0593	0.0343	-0.0127	0.0463	0.0299	0.0236	0.0093	0.0413	0.3592	0.3591	-0.1218	-0.502	0.3005	0.4726	-0.0002	0.4803	0.0089	-0.0266	0.3413	-0.0069	0.3419	7.0531	-54.8042	-30.8588

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 71:87)
2	X-RAY DIFFRACTION	2	(chain A and resid 88:105)
3	X-RAY DIFFRACTION	3	(chain A and resid 106:192)
4	X-RAY DIFFRACTION	4	(chain A and resid 193:230)
5	X-RAY DIFFRACTION	5	(chain A and resid 231:243)
6	X-RAY DIFFRACTION	6	(chain A and resid 244:334)
7	X-RAY DIFFRACTION	7	(chain A and resid 335:345)
8	X-RAY DIFFRACTION	8	(chain A and resid 346:410)
9	X-RAY DIFFRACTION	9	(chain A and resid 411:441)
10	X-RAY DIFFRACTION	10	(chain A and resid 442:485)
11	X-RAY DIFFRACTION	11	(chain B and resid 71:102)
12	X-RAY DIFFRACTION	12	(chain B and resid 103:144)
13	X-RAY DIFFRACTION	13	(chain B and resid 145:207)
14	X-RAY DIFFRACTION	14	(chain B and resid 208:239)
15	X-RAY DIFFRACTION	15	(chain B and resid 240:269)
16	X-RAY DIFFRACTION	16	(chain B and resid 270:360)
17	X-RAY DIFFRACTION	17	(chain B and resid 361:425)
18	X-RAY DIFFRACTION	18	(chain B and resid 426:443)
19	X-RAY DIFFRACTION	19	(chain B and resid 444:475)
20	X-RAY DIFFRACTION	20	(chain B and resid 476:485)
21	X-RAY DIFFRACTION	21	(chain C and resid 1666:1670)
22	X-RAY DIFFRACTION	22	(chain C and resid 1671:1676)
23	X-RAY DIFFRACTION	23	(chain C and resid 1677:1686)
24	X-RAY DIFFRACTION	24	(chain D and resid 1666:1670)
25	X-RAY DIFFRACTION	25	(chain D and resid 1671:1678)
26	X-RAY DIFFRACTION	26	(chain D and resid 1679:1686)

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Yorodumi