PDB-4bqk: rice importin_alpha : VirD2NLS complex

ID or keywords:

Entry

Database: PDB / ID: 4bqk

Title

rice importin_alpha : VirD2NLS complex

Components

IMPORTIN SUBUNIT ALPHA-1A
T-DNA BORDER ENDONUCLEASE VIRD2

Keywords

TRANSPORT PROTEIN / HYDROLASE / NUCLEAR LOCALIZATION SIGNAL

Function / homology

Function and homology information

symbiont-mediated induction of tumor or growth in host / import into nucleus / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / DNA endonuclease activity / Hydrolases; Acting on ester bonds / perinuclear region of cytoplasm / DNA binding / nucleus
Similarity search - Function

Biological species

ORYZA SATIVA (Asian cultivated rice)

AGROBACTERIUM TUMEFACIENS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.997 Å

Authors

Chang, C.-W. / Counago, R.M. / Williams, S.J. / Kobe, B.

Citation

Journal: Mol.Plant / Year: 2014
Title: Structural Basis of Interaction of Bipartite Nuclear Localization Signal from Agrobacterium Vird2 with Rice Importin-Alpha
Authors: Chang, C.-W. / Williams, S.J. / Counago, R.M. / Kobe, B.

History

Deposition	May 31, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 18, 2014	Group: Database references
Revision 2.0	Dec 20, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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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PDBx/mmCIF format	4bqk.cif.gz	484.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4bqk_validation.pdf.gz	471.1 KB	Display	wwPDB validaton report
Full document	4bqk_full_validation.pdf.gz	483.1 KB	Display
Data in XML	4bqk_validation.xml.gz	36.9 KB	Display
Data in CIF	4bqk_validation.cif.gz	52.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bq/4bqk ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bqk	HTTPS FTP

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Related structure data

Related structure data	4bplC 4b8oS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1bk6-1 4b8o-d 2yns-2 2yns-1 4bpl-d 4b8j-d 1un0-2 4zdu-d 1bk6-2 4rxh-d 3tj3-2 3j9s-d 5k9s-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 (11) #205 - Jan 2017 Nuclear Pore Complex similarity (2) #99 - Mar 2008 Cadherin similarity (4) #88 - Apr 2007 Clathrin similarity (2)

Deposited unit

A: IMPORTIN SUBUNIT ALPHA-1A

B: IMPORTIN SUBUNIT ALPHA-1A

C: T-DNA BORDER ENDONUCLEASE VIRD2

D: T-DNA BORDER ENDONUCLEASE VIRD2

hetero molecules

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

1

A: IMPORTIN SUBUNIT ALPHA-1A

D: T-DNA BORDER ENDONUCLEASE VIRD2

hetero molecules

defined by author&software
52.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: IMPORTIN SUBUNIT ALPHA-1A

C: T-DNA BORDER ENDONUCLEASE VIRD2

hetero molecules

defined by author&software
52.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.803, 140.948, 72.632
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 71:494 )
2	1	1	CHAIN B AND (RESSEQ 73:494 )
1	1	2	CHAIN D AND (RESSEQ 416:434 )
2	1	2	CHAIN C AND (RESSEQ 415:434 )

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-1, 0.005, 0.0005), (0.0005, -1, 0.0047), (0.0005, 0.0047, 1)	64.7275, -1.0477, 36.2711

#1: Protein	IMPORTIN SUBUNIT ALPHA-1A Mass: 49384.930 Da / Num. of mol.: 2 / Fragment: RESIDUES 73-526 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Plasmid: PET30A_RIMPALPHA1A_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4
#2: Protein/peptide	T-DNA BORDER ENDONUCLEASE VIRD2 / VIRD2NLS Mass: 2462.657 Da / Num. of mol.: 2 / Fragment: RESIDUES 415-434 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Plasmid: PGEX2T-VIRD2NLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P18592, Hydrolases; Acting on ester bonds
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 395 / 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: 3.1 Å³/Da / Density % sol: 60.32 % / Description: NONE
Crystal grow	pH: 6.5 Details: 16 % PEG3350, 0.1 M BIS-TRISPROPANE PH 6.5, 0.2 M NAF, 0.2 M NDSB-221

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Data collection

Diffraction	Mean temperature: 300 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9536 Å / Relative weight: 1
Reflection	Resolution: 2→19.72 Å / Num. obs: 85023 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / B_iso Wilson estimate: 22.8 Å² / R_merge(I) obs: 0.14 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2→2.11 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.1_1168)	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B8O

4b8o

Resolution: 1.997→19.724 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 22.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2242	4212	5 %
R_work	0.1957	-	-
obs	0.1972	84110	98.59 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.997→19.724 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6705	0	63	395	7163

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	3856	X-RAY DIFFRACTION	POSITIONAL
1	2	B	3856	X-RAY DIFFRACTION	POSITIONAL	0.214
2	1	D	3856	X-RAY DIFFRACTION	POSITIONAL
2	2	C	3856	X-RAY DIFFRACTION	POSITIONAL	0.224

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 (%)
1.9975-2.0201	0.3794	136	0.3252	2468	X-RAY DIFFRACTION	90
2.0201-2.0439	0.3077	128	0.2734	2707	X-RAY DIFFRACTION	100
2.0439-2.0688	0.2846	133	0.2525	2660	X-RAY DIFFRACTION	100
2.0688-2.0949	0.2813	134	0.2328	2716	X-RAY DIFFRACTION	100
2.0949-2.1225	0.2561	160	0.2147	2641	X-RAY DIFFRACTION	100
2.1225-2.1515	0.2643	142	0.2059	2716	X-RAY DIFFRACTION	100
2.1515-2.1822	0.3222	154	0.2531	2685	X-RAY DIFFRACTION	100
2.1822-2.2147	0.4102	139	0.394	2581	X-RAY DIFFRACTION	97
2.2147-2.2493	0.5529	121	0.5548	2235	X-RAY DIFFRACTION	82
2.2493-2.2861	0.5967	130	0.5102	2514	X-RAY DIFFRACTION	94
2.2861-2.3255	0.3095	138	0.2834	2705	X-RAY DIFFRACTION	99
2.3255-2.3677	0.2243	139	0.1742	2647	X-RAY DIFFRACTION	100
2.3677-2.4132	0.1901	147	0.1612	2713	X-RAY DIFFRACTION	100
2.4132-2.4623	0.2149	134	0.1572	2708	X-RAY DIFFRACTION	100
2.4623-2.5158	0.2174	131	0.1581	2724	X-RAY DIFFRACTION	100
2.5158-2.5742	0.2021	141	0.1559	2627	X-RAY DIFFRACTION	100
2.5742-2.6384	0.2202	148	0.1579	2723	X-RAY DIFFRACTION	100
2.6384-2.7096	0.1935	155	0.1588	2705	X-RAY DIFFRACTION	100
2.7096-2.7891	0.1766	134	0.1521	2694	X-RAY DIFFRACTION	100
2.7891-2.8789	0.1856	135	0.1518	2704	X-RAY DIFFRACTION	100
2.8789-2.9814	0.1827	130	0.1525	2735	X-RAY DIFFRACTION	100
2.9814-3.1003	0.219	148	0.1522	2725	X-RAY DIFFRACTION	100
3.1003-3.2409	0.1839	147	0.1606	2631	X-RAY DIFFRACTION	100
3.2409-3.4109	0.1798	127	0.16	2735	X-RAY DIFFRACTION	100
3.4109-3.6234	0.1632	141	0.1639	2716	X-RAY DIFFRACTION	100
3.6234-3.9012	0.1834	147	0.1677	2633	X-RAY DIFFRACTION	97
3.9012-4.2901	0.1519	140	0.1388	2728	X-RAY DIFFRACTION	100
4.2901-4.9025	0.1509	162	0.133	2663	X-RAY DIFFRACTION	100
4.9025-6.1455	0.2	146	0.1723	2734	X-RAY DIFFRACTION	100
6.1455-19.7254	0.1774	145	0.1671	2725	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	2.7476	-0.6939	1.1406	4.2103	0.1202	4.8601	-0.0783	-0.1045	0.0469	0.3458	0.011	-0.0162	-0.2989	0.0453	0.1053	0.3175	-0.0226	0.0085	0.1429	-0.0338	0.3269	50.2868	31.2805	28.3767
2	1.7027	0.9205	0.2188	3.1849	-0.2262	2.1591	-0.0069	-0.0193	0.0846	0.0973	-0.0156	-0.1674	-0.1285	0.0372	0.0103	0.1464	-0.0028	0.0187	0.1614	-0.019	0.1993	46.7028	15.979	24.848
3	4.0796	0.1986	0.5813	4.0911	0.2648	4.5401	0.057	0.0875	-0.0004	0.1055	-0.2401	0.0167	0.6279	-0.2503	0.0483	0.1867	-0.051	0.0322	0.1782	0.0246	0.1422	40.1939	2.1832	30.9668
4	2.9626	1.1168	0.0149	1.1517	-0.3856	0.7258	-0.0088	0.1088	-0.0856	-0.0277	0.0435	0.0077	-0.0532	-0.03	-0.0472	0.1183	0.0027	0.0158	0.1543	0.002	0.1626	21.4694	-8.372	38.153
5	4.9014	1.0896	-0.5299	1.0151	1.0068	1.6943	0.1751	-0.1699	-0.2255	0.6245	-0.3863	0.2031	0.6443	0.033	-0.0419	0.4556	-0.0595	0.0236	0.2551	0.0932	0.3808	15.1985	-32.5841	-8.8833
6	0.9441	0.5656	0.3701	2.609	0.4267	1.5216	0.0232	-0.1557	-0.1136	0.1484	-0.0549	0.1307	0.2527	-0.0302	-0.0075	0.1975	-0.0199	0.0187	0.1952	0.017	0.2112	18.0393	-17.0349	-11.891
7	3.2688	-0.8368	-0.3091	4.1679	0.4373	4.6307	0.0377	-0.0367	-0.0462	0.206	-0.1224	0.0181	-0.4295	-0.0115	0.0098	0.1856	-0.0686	-0.0148	0.1737	-0.0272	0.1158	24.4567	-3.0647	-5.3333
8	1.9438	0.2596	0.7095	0.3002	0.6442	1.752	0.1218	0.0451	-0.3671	-0.0019	0.134	0.3521	0.1672	-0.318	-0.0742	0.1544	-0.0155	-0.0387	0.3008	0.0642	0.4156	-4.9326	-16.7363	33.9905
9	3.5322	1.6032	-1.101	6.3606	-2.294	2.7212	0.307	1.0354	-0.8233	-0.4619	0.0473	-0.244	0.5564	0.0569	-0.058	0.2652	0.0491	-0.1643	0.4508	-0.0456	0.5042	-7.7748	-17.034	22.3399
10	2.7594	0.9659	0.1908	1.272	0.3573	0.8635	-0.0011	0.0402	0.1029	-0.0518	0.0431	-0.0394	0.0754	0.0161	-0.0372	0.1476	-0.0033	0.031	0.1994	-0.0166	0.1932	43.1749	7.5435	1.8215
11	1.0856	0.1199	-0.4808	0.3521	-0.5939	1.5222	0.1605	0.0823	0.37	-0.0039	0.0201	-0.3499	-0.141	0.381	0.0535	0.178	-0.0365	0.0912	0.4039	-0.0662	0.4508	69.5541	15.9407	-2.4021
12	2.665	1.8765	1.1878	6.317	0.7055	2.6233	0.0492	0.7973	0.4722	-0.6689	0.3735	0.3228	-0.6378	0.109	-0.0741	0.3225	0.0129	0.2084	0.5906	0.0894	0.5129	72.4192	16.1105	-14.0508

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 73 THROUGH 104 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 105 THROUGH 209 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 210 THROUGH 241 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 242 THROUGH 404 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 73 THROUGH 104 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 105 THROUGH 209 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 210 THROUGH 241 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 405 THROUGH 476 )
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 477 THROUGH 494 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 242 THROUGH 404 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 405 THROUGH 476 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 477 THROUGH 494 )

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