PDB-4mz6: Structure of importin-alpha: dUTPase S11E NLS mutant complex

ID or keywords:

Entry

Database: PDB / ID: 4mz6

Title

Structure of importin-alpha: dUTPase S11E NLS mutant complex

Components

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

Keywords

PROTEIN TRANSPORT / ARM repeat /

Importin /

nucleus

Function / homology

Function and homology information

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

dUTP diphosphatase /

dUTP diphosphatase activity / NLS-dependent protein nuclear import complex ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.88 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: 4FDS
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

-
Download

PDBx/mmCIF format	4mz6.cif.gz	190.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4mz6.ent.gz	151.8 KB	Display	PDB format
PDBx/mmJSON format	4mz6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mz/4mz6 ftp://data.pdbj.org/pub/pdb/validation_reports/mz/4mz6	HTTPS FTP

-
Related structure data

Related structure data	4mz5C 1elj 3ukw C: citing same article (ref.)
Similar structure data	4u5u-d 3zio-d 5ctt-d 7l04-d 4oih-d 4u5l-d 5x8n-d 5u5p-d 4mz5-d 4htv-d 3ukx-d 5svz-d 3knd-d 4yi0-d 7jjm-d 3uvu-d 3zin-d 2ynr-d 5w4e-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

-
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

58 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)	78.033, 89.948, 99.440
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: 1426.640 Da / Num. of mol.: 2 / Fragment: UNP residues 97-109 / Mutation: S99E / 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.: 336 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 59.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium citrate, DTT, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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: 1.88→99.44 Å / Num. all: 57564 / Num. obs: 57564 / % possible obs: 99.9 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4
Reflection shell	Resolution: 1.88→1.98 Å / % possible all: 100

-
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: 1.88→38.966 Å / SU ML: 0.29 / σ(F): 1.09 / Phase error: 19.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1951	2916	5.08 %	random
R_work	0.1739	-	-	-
obs	0.175	57564	99.9 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.12 Å² / k_sol: 0.367 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.9243 Å²	-0 Å²	0 Å²
2-	-	-5.32 Å²	-0 Å²
3-	-	-	7.2443 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→38.966 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3377	0	0	336	3713

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3445
X-RAY DIFFRACTION	f_angle_d	1.496	4689
X-RAY DIFFRACTION	f_dihedral_angle_d	13.982	1273
X-RAY DIFFRACTION	f_chiral_restr	0.109	562
X-RAY DIFFRACTION	f_plane_restr	0.008	602

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 (%)
1.88-1.9014	0.4132	164	0.3675	3548	X-RAY DIFFRACTION	100
1.9014-1.9238	0.3132	202	0.3202	3450	X-RAY DIFFRACTION	100
1.9238-1.9472	0.3492	207	0.3286	3484	X-RAY DIFFRACTION	100
1.9472-1.9719	0.3117	150	0.2868	3461	X-RAY DIFFRACTION	100
1.9719-1.9978	0.2909	231	0.2579	3519	X-RAY DIFFRACTION	100
1.9978-2.0252	0.268	161	0.2252	3401	X-RAY DIFFRACTION	100
2.0252-2.0541	0.251	179	0.2295	3551	X-RAY DIFFRACTION	100
2.0541-2.0848	0.2606	181	0.2084	3435	X-RAY DIFFRACTION	100
2.0848-2.1173	0.2594	203	0.1957	3478	X-RAY DIFFRACTION	100
2.1173-2.152	0.2501	174	0.198	3487	X-RAY DIFFRACTION	100
2.152-2.1892	0.209	186	0.1819	3457	X-RAY DIFFRACTION	100
2.1892-2.229	0.205	178	0.1778	3512	X-RAY DIFFRACTION	100
2.229-2.2718	0.2418	168	0.1772	3477	X-RAY DIFFRACTION	100
2.2718-2.3182	0.2138	205	0.1679	3468	X-RAY DIFFRACTION	100
2.3182-2.3686	0.199	222	0.1663	3478	X-RAY DIFFRACTION	100
2.3686-2.4237	0.2078	178	0.1728	3524	X-RAY DIFFRACTION	100
2.4237-2.4843	0.2319	189	0.1712	3426	X-RAY DIFFRACTION	100
2.4843-2.5514	0.2348	204	0.1659	3420	X-RAY DIFFRACTION	100
2.5514-2.6265	0.1573	155	0.1688	3534	X-RAY DIFFRACTION	100
2.6265-2.7113	0.1795	185	0.1623	3480	X-RAY DIFFRACTION	100
2.7113-2.8081	0.1811	197	0.1565	3497	X-RAY DIFFRACTION	100
2.8081-2.9205	0.2101	136	0.1642	3511	X-RAY DIFFRACTION	100
2.9205-3.0534	0.1993	189	0.1734	3479	X-RAY DIFFRACTION	100
3.0534-3.2143	0.1986	183	0.1722	3491	X-RAY DIFFRACTION	100
3.2143-3.4156	0.1843	186	0.1767	3452	X-RAY DIFFRACTION	100
3.4156-3.6791	0.1618	193	0.17	3484	X-RAY DIFFRACTION	100
3.6791-4.049	0.1689	200	0.1499	3456	X-RAY DIFFRACTION	100
4.049-4.6341	0.1632	209	0.1327	3445	X-RAY DIFFRACTION	100
4.6341-5.8353	0.1726	180	0.1531	3490	X-RAY DIFFRACTION	100
5.8353-38.966	0.1608	192	0.1795	3435	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	2.5548	0.4335	-0.5864	0.1454	0.39	3.4473	0.0788	0.528	0.1108	-0.4408	0.2647	-0.0752	-0.2817	0.3157	-0.1634	0.4558	-0.0259	0.0766	0.4615	-0.2122	0.7042	40.8359	60.0847	40.5196
2	4.6075	-0.4846	0.0577	7.3443	3.7368	1.9954	0.2471	0.5119	-0.5287	0.2301	-0.6092	1.1848	0.3253	-0.6168	0.4815	0.303	0.0138	-0.0024	0.3073	-0.0493	0.4156	35.7999	84.8845	58.9276
3	1.6771	-0.2982	-0.4762	3.6054	1.3318	1.024	0.1406	-0.0453	0.1566	-0.0724	-0.0447	0.0627	-0.2128	-0.0857	-0.093	0.2233	-0.0026	0.0518	0.1707	-0.0028	0.1263	45.6875	92.7125	65.4142
4	1.9206	0.7209	0.6001	1.7251	0.5772	1.6649	0.1165	0.0178	-0.2618	0.1129	-0.0163	0.0199	0.0811	-0.0229	-0.0975	0.1741	-0.0086	-0.0049	0.1446	0.018	0.214	38.528	66.4824	61.5676
5	2.6992	0.5137	1.2685	2.8508	0.5563	2.0873	0.064	0.8138	-0.3689	-0.4327	0.2372	-0.5908	0.1095	0.5468	-0.1117	0.2378	0.0294	0.0623	0.4101	-0.1717	0.3708	31.4109	51.9511	31.2491

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 13:19 )	A	13 - 19
2	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 11:20 )	C	11 - 20
3	X-RAY DIFFRACTION	3	( CHAIN E AND RESID 72:202 )	E	72 - 202
4	X-RAY DIFFRACTION	4	( CHAIN E AND RESID 203:322 )	E	203 - 322
5	X-RAY DIFFRACTION	5	( CHAIN E AND RESID 323:497 )	E	323 - 497

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi