PDB-4eij: Structure of the Mumps virus phosphoprotein oligomerization domain

ID or keywords:

Entry

Database: PDB / ID: 4eij

Title

Structure of the Mumps virus phosphoprotein oligomerization domain

Components

P protein

Keywords

REPLICATION / oligomerization

Function / homology

Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / Phosphoprotein

Function and homology information

Biological species

Mumps virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.2001 Å

Authors

Cox, R. / Green, T.J. / Luo, M.

Citation

Journal: J.Virol. / Year: 2013
Title: Structural and functional characterization of the mumps virus phosphoprotein.
Authors: Cox, R. / Green, T.J. / Purushotham, S. / Deivanayagam, C. / Bedwell, G.J. / Prevelige, P.E. / Luo, M.

History

Deposition	Apr 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2013	Group: Database references
Revision 1.2	Jun 26, 2013	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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Download

PDBx/mmCIF format	4eij.cif.gz	62.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4eij.ent.gz	49 KB	Display	PDB format
PDBx/mmJSON format	4eij.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4eij_validation.pdf.gz	436.6 KB	Display	wwPDB validaton report
Full document	4eij_full_validation.pdf.gz	436.6 KB	Display
Data in XML	4eij_validation.xml.gz	7.4 KB	Display
Data in CIF	4eij_validation.cif.gz	9.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/4eij ftp://data.pdbj.org/pub/pdb/validation_reports/ei/4eij	HTTPS FTP

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Related structure data

Similar structure data	6ufe-d 4r6z-d 3f42-1 3t4z-d 4pdv-d 4kze-3 4pdl-d 3e8b-d 1gnk-d 4ad7-1 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#231 - Mar 2019 Measles Virus Proteins similarity (2)

Deposited unit

A: P protein

B: P protein

hetero molecules

14.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: P protein

B: P protein

hetero molecules

A: P protein

B: P protein

hetero molecules

defined by author&software
28.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: P protein

B: P protein

hetero molecules

A: P protein

B: P protein

hetero molecules

A: P protein

B: P protein

hetero molecules

defined by software
43.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.348, 80.348, 165.170
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-419- HOH
2	1	A-420- HOH
3	1	A-424- HOH
4	1	B-326- HOH
5	1	B-328- HOH
6	1	B-331- HOH

#1: Protein	P protein Mass: 7183.435 Da / Num. of mol.: 2 / Fragment: Oligomerization Domain (UNP Residues 213-277) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mumps virus / Strain: 88-1961 / Gene: P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8QY72
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.57 Å³/Da / Density % sol: 65.55 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate pH 4.6, 2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2010
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 10717 / Num. obs: 10717 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / R_sym value: 0.062 / Net I/σ(I): 26.69
Reflection shell	Resolution: 2.2→2.4 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 4.14 / Num. unique all: 528 / % possible all: 100

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Phasing

Phasing	Method: SIRAS

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
CNS		phasing
RESOLVE		phasing
PHENIX	1.6_289	refinement
PDB_EXTRACT	3.11	data extraction
SERGUI		data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

SIRAS / Resolution: 2.2001→26.607 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8474 / SU ML: 0.26 / σ(F): 0.12 / Phase error: 21.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2302	1029	9.98 %	Random
R_work	0.1814	-	-	-
obs	0.1864	10308	96.15 %	-
all	-	10308	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.815 Å² / k_sol: 0.351 e/Å³

Displacement parameters

B_iso max: 123.56 Å² / B_iso mean: 43.2547 Å² / B_iso min: 16.55 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.5535 Å²	0 Å²	-0 Å²
2-	-	6.5535 Å²	0 Å²
3-	-	-	-13.1069 Å²

Refinement step

Cycle: LAST / Resolution: 2.2001→26.607 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	942	0	6	58	1006

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	947
X-RAY DIFFRACTION	f_angle_d	0.887	1268
X-RAY DIFFRACTION	f_chiral_restr	0.06	165
X-RAY DIFFRACTION	f_plane_restr	0.003	156
X-RAY DIFFRACTION	f_dihedral_angle_d	15.9	367

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2001-2.316	0.2772	135	0.2032	1225	1360	90
2.316-2.461	0.2807	140	0.2083	1249	1389	93
2.461-2.6509	0.2498	145	0.1936	1308	1453	95
2.6509-2.9174	0.207	145	0.182	1328	1473	97
2.9174-3.3388	0.2246	150	0.1779	1357	1507	99
3.3388-4.2039	0.2188	154	0.1557	1375	1529	99
4.2039-26.6084	0.217	160	0.185	1437	1597	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	2.4624	3.0116	-3.2965	3.677	-3.9977	4.409	-0.7234	0.3938	-1.5744	-1.8058	0.2465	-0.8347	2.0193	0.9704	0.0702	0.3192	0.0261	0.093	0.5189	-0.0753	0.3678	32.4342	55.706	42.9845
2	5.2908	-3.9074	1.9083	8.0712	-0.647	3.9463	-0.0488	0.4317	-1.2301	0.5446	0.9003	0.7726	1.0911	0.6378	-0.6334	0.2825	0.0404	-0.0528	0.1915	-0.0595	0.2709	29.3994	55.3289	49.6735
3	4.0907	1.3524	4.994	0.8741	1.5999	6.2563	-0.1981	-0.1281	-1.1392	-0.2369	0.6679	0.1226	-0.8837	0.8587	-0.7109	0.267	0.0097	0.0382	0.5728	0.0125	0.3054	28.6758	53.3447	57.9387
4	5.9661	-4.3881	-2.718	6.086	4.1198	3.5114	-0.1274	-1.2152	-0.1041	0.4991	-0.2192	1.1966	0.569	0.1253	0.253	0.2027	-0.0603	-0.098	0.3503	0.0221	0.2225	26.9233	53.8241	66.0246
5	0.775	-1.6219	-2.1578	6.1421	8.3395	2.0005	0.2838	0.1687	-0.2709	0.0703	-0.7108	0.9171	1.3578	-1.6827	-0.1208	0.1798	-0.051	-0.0508	0.3315	0.1168	0.2853	26.7855	52.7706	74.2199
6	8.1133	1.985	-2.9101	5.3109	-3.62	2.7845	-0.5333	-0.9113	0.6377	0.9965	1.139	0.2218	0.6386	-2.0792	-0.5811	0.3669	0.0582	-0.0425	0.4541	0.0587	0.3764	26.2592	55.4086	85.5489
7	0.5332	-0.7219	-1.9787	6.5821	1.7978	7.4698	0.1821	0.3032	0.1857	0.756	-0.3684	-0.0184	0.1589	-2.2399	0.1376	0.4588	0.2077	-0.0992	0.4742	-0.0987	0.2457	27.9294	58.7443	95.3453
8	0.2187	-0.8847	-0.0556	5.132	-0.0082	0.0482	0.3134	0.1909	0.3912	-0.1439	-0.1934	-0.0355	-0.3706	-0.0138	0.1931	0.3385	0.1862	-0.052	0.2983	-0.0408	0.2659	31.3618	61.9834	105.2104
9	1.7478	-0.0744	0.326	1.9108	0.0909	1.9896	-0.0419	0.0793	0.3292	-0.34	0.1396	-0.108	0.0336	-0.1308	0.1759	0.2083	-0.0119	-0.0274	0.1796	-0.0303	0.2403	34.8613	64.8867	116.4542
10	7.7806	-4.6451	-5.2094	7.778	4.9132	7.3844	-0.3461	-0.7018	-0.4493	0.3108	-0.5726	1.0052	-0.4746	0.0204	-0.613	0.5666	0.2264	-0.2652	0.2728	-0.1976	0.2578	32.7948	78.0801	125.7338
11	6.8725	5.0849	2.6634	4.2898	3.6621	6.4597	-0.7702	1.9645	-1.1721	-1.3764	2.4546	-1.3457	-1.5193	0.2749	-0.9669	0.4143	-0.2736	0.0595	0.5254	-0.1026	0.3021	22.0783	61.9743	40.1814
12	2.7185	2.9171	0.4557	3.6	0.7509	8.3507	-0.5894	-0.1334	0.5169	0.1356	-0.087	1.4216	0.668	-1.6326	0.2723	0.1379	-0.0599	-0.0349	0.2989	0.0045	0.3694	22.0622	62.4913	48.3466
13	1.0646	-1.2298	2.2021	1.6569	-2.9606	5.267	-0.2525	-0.2401	0.7492	0.4324	0.1779	-0.0041	-1.0615	-1.3435	0.1394	0.1948	0.0052	0.0042	0.4026	-0.0325	0.2314	24.3029	63.007	56.0858
14	5.8382	-3.0473	6.4343	4.2323	-0.9601	9.2894	-1.1103	0.2531	1.2015	0.8653	0.2217	0.0474	-0.4017	1.0507	0.8796	0.2075	-0.0551	0.0321	0.3934	-0.0259	0.2999	24.0316	62.8148	65.2454
15	4.6545	3.059	-2.4191	4.0471	-5.213	7.7877	0.3741	0.0086	1.1429	0.5603	-0.1625	0.8514	-1.414	0.1271	0.6266	0.2109	-0	-0.033	0.3006	0.0285	0.2886	26.9773	64.1268	72.5296
16	5.4745	-4.5348	3.9925	5.771	-0.5099	6.7825	-1.4101	0.0506	0.1839	2.3061	0.1421	0.2515	-0.4818	0.2002	0.4821	0.4801	-0.0439	-0.1096	0.2463	0.0238	0.2956	29.5332	63.0857	81.1181
17	5.1715	-0.756	2.7163	2.0192	-1.3825	7.2321	-1.2994	-0.6269	1.0028	0.9099	-0.1677	-0.1501	-1.674	-0.2064	1.2176	0.9327	0.2577	-0.2417	0.1285	-0.0599	0.3446	33.7798	64.0861	90.308
18	5.6104	5.6426	5.3549	6.141	6.5618	8.7599	-1.4149	-0.227	1.3119	-1.8496	0.6428	0.7951	-2.1491	0.5959	0.4238	0.8614	0.1402	-0.0814	0.2198	-0.0003	0.3788	38.8336	63.8093	97.4901
19	2.5567	-1.8913	-0.2128	5.3459	3.4254	2.9083	0.4329	0.3807	0.5218	-1.1161	-0.1822	-0.8067	0.2337	-0.1757	0.1443	0.3133	0.017	0.0482	0.2626	0.0388	0.2209	42.0602	62.2991	107.0357
20	1.8527	1.4581	-1.155	5.722	-0.0566	6.1924	-0.1993	-0.4191	-0.6863	0.2821	-0.296	-0.985	1.5914	-0.1018	0.3983	0.2442	-0.0669	0.0185	0.2007	0.0754	0.2265	44.3678	60.1486	117.7435

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 215:220)	A	215 - 220
2	X-RAY DIFFRACTION	2	(chain A and resid 221:225)	A	221 - 225
3	X-RAY DIFFRACTION	3	(chain A and resid 226:231)	A	226 - 231
4	X-RAY DIFFRACTION	4	(chain A and resid 232:236)	A	232 - 236
5	X-RAY DIFFRACTION	5	(chain A and resid 237:242)	A	237 - 242
6	X-RAY DIFFRACTION	6	(chain A and resid 243:249)	A	243 - 249
7	X-RAY DIFFRACTION	7	(chain A and resid 250:256)	A	250 - 256
8	X-RAY DIFFRACTION	8	(chain A and resid 257:263)	A	257 - 263
9	X-RAY DIFFRACTION	9	(chain A and resid 264:272)	A	264 - 272
10	X-RAY DIFFRACTION	10	(chain A and resid 273:277)	A	273 - 277
11	X-RAY DIFFRACTION	11	(chain B and resid 213:218)	B	213 - 218
12	X-RAY DIFFRACTION	12	(chain B and resid 219:223)	B	219 - 223
13	X-RAY DIFFRACTION	13	(chain B and resid 224:229)	B	224 - 229
14	X-RAY DIFFRACTION	14	(chain B and resid 230:234)	B	230 - 234
15	X-RAY DIFFRACTION	15	(chain B and resid 235:240)	B	235 - 240
16	X-RAY DIFFRACTION	16	(chain B and resid 241:246)	B	241 - 246
17	X-RAY DIFFRACTION	17	(chain B and resid 247:252)	B	247 - 252
18	X-RAY DIFFRACTION	18	(chain B and resid 253:258)	B	253 - 258
19	X-RAY DIFFRACTION	19	(chain B and resid 259:265)	B	259 - 265
20	X-RAY DIFFRACTION	20	(chain B and resid 266:273)	B	266 - 273

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