PDB-4mz5: Structure of importin-alpha: dUTPase NLS complex

ID or keywords:

Entry

Database: PDB / ID: 4mz5

Title

Structure of importin-alpha: dUTPase NLS complex

Components

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
Importin subunit alpha-1

Keywords

PROTEIN TRANSPORT / ARM repeat /

Importin /

nucleus

Function / homology

Function and homology information

Sensing of DNA Double Strand Breaks / dUTP catabolic process / entry of viral genome into host nucleus through nuclear pore complex via importin / dUMP biosynthetic process / positive regulation of viral life cycle /

dUTP diphosphatase /

dUTP diphosphatase activity / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / Interconversion of nucleotide di- and triphosphates ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Marfori, M. / Rona, G. / Vertessy, B.G. / Kobe, B.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights.
Authors: Rona, G. / Marfori, M. / Borsos, M. / Scheer, I. / Takacs, E. / Toth, J. / Babos, F. / Magyar, A. / Erdei, A. / Bozoky, Z. / Buday, L. / Kobe, B. / Vertessy, B.G.

History

Deposition	Sep 29, 2013	Deposition site: RCSB / Processing site: RCSB
Supersession	Nov 13, 2013	ID: 4FDR
Revision 1.0	Nov 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2013	Group: Derived calculations
Revision 1.2	Dec 11, 2013	Group: Database references
Revision 1.3	Sep 24, 2014	Group: Database references
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4mz5.cif.gz	189.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mz/4mz5 ftp://data.pdbj.org/pub/pdb/validation_reports/mz/4mz5	HTTPS FTP

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Related structure data

Related structure data	4mz6C 1elj 3ukw C: citing same article (ref.)
Similar structure data	5ctt-d 5x8n-d 6bw0-d 4u58-d 4oih-d 3knd-d 6wx7-d 4htv-d 5svz-d 3zio-d 3tpo-d 4mz6-d 4u54-d 4tnm-d 3wpt-1 1q1t-d 6bw1-d 4u5n-d 7l04-d 3ve6-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 (12) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (5) #205 - Jan 2017 Nuclear Pore Complex similarity (2) #99 - Mar 2008 Cadherin similarity (4) #88 - Apr 2007 Clathrin similarity (2) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1)

Deposited unit

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial

C: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial

E: Importin subunit alpha-1

57.9 kDa, 3 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)	77.876, 89.995, 99.729
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

THE PROTEIN IMPORTIN ALPHA HAS A TWO BINDING SITES ON THE SURFACE OF THE MOLECULE. THERE IS EXTENSIVE LITERATURE THAT SHOWS THAT 'BIPARTITE' PEPTIDES CAN BIND TO BOTH BINDING SITES SIMULTANEOUSLY, WHILE SHORTER 'MONOPARTITE' PEPTIDES SUCH AS THE ONES USED IN THIS STUDY, BIND TO ONLY ONE. WE THEREFORE BELIEVE THAT THE PRESENCE OF THE PEPTIDE AT BOTH BINDING SITES IS THE RESULT OF CRYSTALLIZATION ARTIFACTS DUE TO THE CONCENTRATION OF PEPTIDE USED IN THE STUDY.

#1: Protein/peptide	Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / dUTPase / dUTP pyrophosphatase Mass: 1384.604 Da / Num. of mol.: 2 / Fragment: UNP residues 97-109 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P33316
#2: Protein	Importin subunit alpha-1 / / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha Mass: 55121.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-528 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P52293
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.02 Å³/Da / Density % sol: 59.25 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium citrate, DTT, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953693 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 14, 2011
Radiation	Monochromator: Sagitally focused Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953693 Å / Relative weight: 1
Reflection	Resolution: 2.1→99.73 Å / Num. all: 41431 / Num. obs: 41431 / % possible obs: 99.4 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3
Reflection shell	Resolution: 2.1→2.21 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→42 Å / SU ML: 0.24 / σ(F): 0.9 / Phase error: 24.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2317	2084	5.06 %	random
R_work	0.1987	-	-	-
obs	0.2003	41431	98.43 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 56.58 Å² / k_sol: 0.362 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.8164 Å²	-0 Å²	0 Å²
2-	-	-13.4133 Å²	-0 Å²
3-	-	-	17.2297 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3404	0	0	192	3596

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3464
X-RAY DIFFRACTION	f_angle_d	1.034	4715
X-RAY DIFFRACTION	f_dihedral_angle_d	13.659	1277
X-RAY DIFFRACTION	f_chiral_restr	0.068	566
X-RAY DIFFRACTION	f_plane_restr	0.005	605

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 (%)
2.1-2.1256	0.3505	193	0.3278	2586	X-RAY DIFFRACTION	100
2.1256-2.1525	0.2937	99	0.3085	2734	X-RAY DIFFRACTION	100
2.1525-2.1808	0.2805	114	0.3083	2707	X-RAY DIFFRACTION	100
2.1808-2.2107	0.3214	146	0.2834	2704	X-RAY DIFFRACTION	100
2.2107-2.2423	0.2743	163	0.2767	2588	X-RAY DIFFRACTION	99
2.2423-2.2758	0.3006	153	0.2616	2662	X-RAY DIFFRACTION	99
2.2758-2.3113	0.2692	164	0.2474	2659	X-RAY DIFFRACTION	99
2.3113-2.3492	0.295	121	0.2464	2664	X-RAY DIFFRACTION	100
2.3492-2.3897	0.3265	129	0.2432	2687	X-RAY DIFFRACTION	99
2.3897-2.4332	0.2668	129	0.2301	2700	X-RAY DIFFRACTION	100
2.4332-2.48	0.2604	130	0.2361	2650	X-RAY DIFFRACTION	99
2.48-2.5306	0.3122	151	0.2206	2642	X-RAY DIFFRACTION	99
2.5306-2.5856	0.2857	152	0.2266	2669	X-RAY DIFFRACTION	99
2.5856-2.6457	0.2859	143	0.2274	2643	X-RAY DIFFRACTION	100
2.6457-2.7119	0.2289	144	0.2173	2656	X-RAY DIFFRACTION	100
2.7119-2.7852	0.2122	154	0.2038	2644	X-RAY DIFFRACTION	99
2.7852-2.8671	0.2359	133	0.1976	2683	X-RAY DIFFRACTION	99
2.8671-2.9597	0.2105	155	0.1908	2614	X-RAY DIFFRACTION	99
2.9597-3.0654	0.2771	165	0.1991	2628	X-RAY DIFFRACTION	98
3.0654-3.1881	0.2508	105	0.1972	2662	X-RAY DIFFRACTION	98
3.1881-3.3331	0.2397	174	0.2025	2579	X-RAY DIFFRACTION	97
3.3331-3.5088	0.2179	133	0.1995	2608	X-RAY DIFFRACTION	97
3.5088-3.7285	0.2285	122	0.179	2630	X-RAY DIFFRACTION	97
3.7285-4.0162	0.1816	153	0.1632	2527	X-RAY DIFFRACTION	96
4.0162-4.4199	0.1666	117	0.1482	2577	X-RAY DIFFRACTION	95
4.4199-5.0586	0.1875	112	0.1622	2585	X-RAY DIFFRACTION	96
5.0586-6.3697	0.2288	156	0.1999	2566	X-RAY DIFFRACTION	96
6.3697-42	0.1837	124	0.165	2575	X-RAY DIFFRACTION	96

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	0.0434	0.0229	0.1862	0.0628	0.0527	0.8303	-0.2522	0.2287	0.11	-0.0407	-0.0274	-0.0129	-0.2188	0.1977	-0.0396	0.3503	0.0487	-0.0136	0.3798	-0.1455	0.6441	42.0649	57.0403	40.7396
2	3.3076	0.0678	-2.6627	0.499	-1.2981	5.31	-0.1211	0.0105	-0.2319	-0.1796	-0.2051	1.0819	0.3114	-0.5863	0.4239	0.3443	0.0135	-0.0435	0.2996	-0.1027	0.5578	35.3408	84.0017	58.223
3	3.3967	0.3656	-0.9444	4.1362	1.347	1.4351	0.1427	-0.1243	0.4477	-0.1036	-0.0585	0.1816	-0.2657	-0.0532	0.1924	0.3046	0.0194	0.0847	0.2134	-0.0274	0.2798	43.9712	99.2409	66.2919
4	2.1679	0.9081	0.4265	2.189	0.5715	1.1114	0.1283	-0.0658	-0.3236	0.0707	-0.0294	-0.0377	0.0123	0.0346	0.1262	0.1902	0.0112	0.0147	0.1903	0.0047	0.1753	41.2923	71.5099	62.4868
5	2.1773	0.283	0.8857	2.4729	0.7038	3.1466	0.0513	0.6845	-0.1705	-0.4084	0.1689	-0.5458	0.0747	0.4506	0.2096	0.2471	0.0178	0.0602	0.3973	-0.1412	0.4358	31.5309	51.8931	31.3219

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 11:18)
2	X-RAY DIFFRACTION	2	chain 'C' and (resseq 9:20)
3	X-RAY DIFFRACTION	3	chain 'E' and (resseq 71:148)
4	X-RAY DIFFRACTION	4	chain 'E' and (resseq 149:322)
5	X-RAY DIFFRACTION	5	chain 'E' and (resseq 323:497)

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