PDB-4z3u: PRV nuclear egress complex

ID or keywords:

Entry

Database: PDB / ID: 4z3u

Title

PRV nuclear egress complex

Components

UL31
UL34 protein

Keywords

VIRAL PROTEIN / complex / membrane binding

Function / homology

Function and homology information

host cell nuclear inner membrane / viral budding from nuclear membrane / membrane => GO:0016020 / membrane / metal ion binding
Similarity search - Function

Biological species

Suid herpesvirus 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.706 Å

Authors

Bigalke, J.M. / Heldwein, E.E.

Funding support

United States,

Germany, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	1R01GM111795-01	United States
Burroughs Wellcome Fund
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	1R21AI097573-01A1	United States
German Research Foundation (DFG)	BI 1658/1-1	Germany

Citation

Journal: Embo J. / Year: 2015
Title: Structural basis of membrane budding by the nuclear egress complex of herpesviruses.
Authors: Bigalke, J.M. / Heldwein, E.E.

History

Deposition	Mar 31, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 16, 2015	Group: Database references
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Jan 17, 2018	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4z3u.cif.gz	348.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4z3u.ent.gz	299.6 KB	Display	PDB format
PDBx/mmJSON format	4z3u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4z3u_validation.pdf.gz	464.7 KB	Display	wwPDB validaton report
Full document	4z3u_full_validation.pdf.gz	480.3 KB	Display
Data in XML	4z3u_validation.xml.gz	31.6 KB	Display
Data in CIF	4z3u_validation.cif.gz	42.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z3/4z3u ftp://data.pdbj.org/pub/pdb/validation_reports/z3/4z3u	HTTPS FTP

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Related structure data

Related structure data	4zxsC C: citing same article (ref.)
Similar structure data	1lgc-2 5tni-1 5km0-d 3nnt-d 3lqk-3 1e4y-d 6qhu-d 6de4-d 4bpz-d 3kxp-2 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

Deposited unit

A: UL34 protein

B: UL31

C: UL34 protein

D: UL31

hetero molecules

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

1

A: UL34 protein

B: UL31

hetero molecules

defined by author&software
Evidence: gel filtration, light scattering
49.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: UL34 protein

D: UL31

hetero molecules

defined by author&software
Evidence: gel filtration, light scattering
49.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.456, 125.456, 109.235
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Details

heterodimer in solution (confirmed by gel filtration and MALS)

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Protein , 2 types, 4 molecules ACBD

#1: Protein	UL34 protein Mass: 20244.197 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL34 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G8R3, UniProt: G3G8X8*PLUS
#2: Protein	UL31 / UL31 protein Mass: 28760.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL31 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G955

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Non-polymers , 4 types, 46 molecules

#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3 M NaSCN, 18% PEG3350, 0.3 M NaCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.706→49.907 Å / Num. obs: 24223 / % possible obs: 99.36 % / Redundancy: 4.55 % / R_merge(I) obs: 0.087 / Net I/σ(I): 10.41
Reflection shell	Resolution: 2.706→2.802 Å / Redundancy: 4.21 % / R_merge(I) obs: 0.617 / Mean I/σ(I) obs: 2.02 / % possible all: 96

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PHENIX		phasing
PHENIX		model building
SHELX		phasing
XDS		data scaling
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.706→49.907 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2725	1995	8.24 %
R_work	0.2121	-	-
obs	0.2171	24223	99.35 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.706→49.907 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6554	0	8	38	6600

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6713
X-RAY DIFFRACTION	f_angle_d	0.787	9107
X-RAY DIFFRACTION	f_dihedral_angle_d	12.683	2486
X-RAY DIFFRACTION	f_chiral_restr	0.028	1007
X-RAY DIFFRACTION	f_plane_restr	0.003	1199

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 (%)
2.706-2.7734	0.3964	135	0.3174	1510	X-RAY DIFFRACTION	96
2.7734-2.8484	0.3213	139	0.3026	1546	X-RAY DIFFRACTION	100
2.8484-2.9322	0.3748	140	0.2946	1561	X-RAY DIFFRACTION	100
2.9322-3.0268	0.3459	141	0.2842	1566	X-RAY DIFFRACTION	100
3.0268-3.135	0.2959	141	0.29	1571	X-RAY DIFFRACTION	100
3.135-3.2605	0.31	142	0.2634	1571	X-RAY DIFFRACTION	100
3.2605-3.4088	0.3157	141	0.2416	1574	X-RAY DIFFRACTION	100
3.4088-3.5885	0.2939	142	0.2269	1572	X-RAY DIFFRACTION	100
3.5885-3.8133	0.2954	142	0.2063	1595	X-RAY DIFFRACTION	100
3.8133-4.1076	0.2714	141	0.2026	1576	X-RAY DIFFRACTION	100
4.1076-4.5207	0.2407	146	0.1769	1608	X-RAY DIFFRACTION	100
4.5207-5.1742	0.2077	145	0.1689	1612	X-RAY DIFFRACTION	100
5.1742-6.5167	0.2436	146	0.2039	1645	X-RAY DIFFRACTION	100
6.5167-49.916	0.2599	154	0.1816	1721	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	1.1015	2.907	0.6074	7.7325	2.3523	7.8643	-0.3955	0.6973	-0.482	-0.421	0.2221	-1.0315	0.4936	1.1071	0.1801	0.6378	0.2871	0.206	0.6574	0.0442	0.7143	54.8577	72.758	50.1344
2	9.8781	0.6818	-0.6603	2.4381	-1.9578	2.7156	0.9517	2.1486	-0.7322	-1.464	-0.389	-0.1729	0.2646	-0.1899	-0.265	0.9747	0.5984	-0.117	1.4136	0.0437	0.8799	53.7813	74.4646	43.1584
3	5.026	3.1826	5.4515	4.6066	4.4642	6.3528	-0.9452	0.3593	-0.0291	-0.7888	0.4582	-0.203	-0.7923	2.4001	-0.119	0.4382	-0.0879	-0.1286	1.2839	0.5841	1.3663	63.4895	87.7558	51.893
4	5.3564	2.3369	3.8401	6.2315	0.5072	6.838	-0.7134	0.8341	0.7022	-0.9902	-0.089	-0.4129	-0.2616	1.1787	0.6465	0.4541	0.1296	0.1685	0.6509	0.0724	0.6349	48.5742	79.666	48.5877
5	4.8947	-0.3174	1.1028	2.4519	-0.6358	6.6025	-0.1473	1.3925	1.7119	-0.0413	-0.1394	-0.6549	-0.6972	0.323	0.2317	0.4887	-0.0059	0.0571	0.5433	0.2507	0.8451	46.4412	89.1818	45.6741
6	6.0406	-1.4171	2.4862	4.6385	-0.6286	1.9407	-0.0264	0.5058	0.6222	-0.1739	-0.3775	-0.5624	0.1036	0.4113	0.3524	0.3947	0.0116	0.0602	0.4002	0.0636	0.5151	39.0813	83.3517	52.3069
7	5.3205	3.7011	6.7259	3.445	3.6271	9.5164	1.7356	-2.6377	-1.0715	2.024	-0.6013	-0.623	2.8557	-0.5599	-1.1113	1.1879	0.0143	-0.1081	1.3531	-0.0439	0.7085	47.2887	70.4059	70.1635
8	4.2859	3.8039	2.0953	4.8403	4.6447	5.735	0.3371	-0.7128	-0.331	-0.6897	0.4839	-0.6333	-0.7291	0.3023	-1.0559	0.5152	0.137	0.1124	0.9447	0.0392	0.7478	52.3253	80.0568	66.5454
9	6.9607	-4.2466	5.2485	4.4369	-2.0455	4.909	0.0816	-0.05	0.1434	-0.105	-0.0881	-0.1878	0.1429	-0.0684	0.0339	0.4207	-0.0224	0.0808	0.3451	-0.004	0.3067	29.7255	79.6207	49.6267
10	4.2798	0.0817	-3.5159	0.156	0.5662	5.5975	-0.3181	0.628	-0.6005	-1.4337	-0.1839	0.4886	0.3168	-0.5561	0.436	0.7737	0.0281	-0.0905	0.5294	-0.0415	0.3726	21.3532	73.5403	43.3159
11	2.6066	0.416	0.0824	2.0434	-1.7632	4.3229	-0.5202	1.3448	-0.3385	0.3284	1.3286	-0.8547	1.9048	0.5332	-0.706	1.2241	0.2308	-0.1929	0.8773	-0.3331	0.718	13.6545	76.3807	18.9134
12	2.7193	0.5648	1.3524	3.5156	3.1643	3.1426	0.4675	1.0766	-0.2145	-0.6744	-0.2534	0.2288	-0.164	-0.1551	-0.1573	0.8859	0.0829	-0.0571	0.6802	-0.0131	0.3534	13.4933	83.0503	22.4864
13	6.545	-2.2984	1.4317	8.2361	-4.4888	8.3727	0.4547	0.3651	0.0222	-0.6037	-0.4654	0.1919	0.2512	0.3406	0.0855	0.5879	0.0398	-0.0373	0.3651	-0.0999	0.3813	17.6777	84.6875	32.4928
14	4.1545	-3.4822	0.347	7.6874	3.4917	4.0961	0.3773	0.0226	1.7778	-0.4533	0.1999	-0.1958	-0.5367	-0.482	-0.5048	0.4989	0.0582	-0.1418	0.5355	0.0593	0.4764	15.8956	90.2427	33.5326
15	0.7684	0.4733	0.1108	2.5375	-1.8129	2.7475	-0.4532	0.2344	0.8462	-0.1327	-0.2701	0.595	0.5975	0.1247	0.0313	0.9421	0.1058	0.1829	1.3002	0.0563	0.9109	26.0729	86.5951	16.0064
16	5.9236	0.4913	-0.1797	6.3926	0.6248	6.4488	-0.091	0.4912	-0.4906	-0.1709	-0.0772	0.0971	0.2712	0.5039	0.0987	0.5367	0.0936	-0.0744	0.6869	-0.0801	0.3725	4.9107	86.4509	22.7232
17	9.2075	-2.2445	0.1684	3.8376	-4.0333	4.8321	0.9186	0.1462	0.6468	-0.2819	0.8179	1.525	-0.9476	-0.8737	-1.8257	0.9172	0.2773	-0.0414	0.8462	-0.1789	0.8189	7.2208	117.7107	59.1353
18	4.2693	3.1319	-2.222	4.8646	-4.8234	4.99	-0.1552	-0.7286	1.6661	1.6004	1.5741	1.9167	-1.0822	-1.1987	-1.4941	0.8884	0.1769	0.046	0.7646	-0.012	1.3235	7.8657	115.5871	66.4906
19	7.7168	-2.1337	2.3404	8.2941	-5.2339	4.8338	0.1962	0.7423	2.4435	-0.2733	-1.3928	-0.4081	-3.1802	0.3803	0.9895	1.4935	-0.1771	-0.344	0.7825	0.2032	1.2121	21.8645	126.7699	58.478
20	3.9296	2.9265	-3.4555	7.4424	-0.346	4.0621	0.0638	-0.6154	0.0075	0.5281	-0.386	0.7159	-1.803	0.6539	0.5904	0.8131	0.0433	-0.1841	0.6199	-0.034	0.711	14.268	111.5992	60.7808
21	6.2582	3.7603	-3.6612	5.4181	-3.7174	3.5048	0.0841	-0.8197	0.4113	0.273	-0.5279	-0.2265	-0.9536	0.9422	0.3342	0.6649	-0.1132	-0.1659	0.5907	0.0312	0.7887	23.1931	114.6706	63.8025
22	9.2958	0.4207	0.3176	3.6713	-2.6224	6.5303	0.3309	0.3186	0.7395	0.2589	-0.5228	-1.6798	0.6286	0.6943	0.216	1.2343	0.1458	-0.195	0.4189	-0.0363	0.3699	24.9696	99.6208	66.1125
23	7.6994	0.9441	2.1721	9.3218	0.1522	8.6858	0.2928	-0.4211	-0.1531	-0.311	-0.5951	-0.6772	-0.9866	0.5605	0.4087	0.4017	-0.0428	-0.0661	0.5123	-0.0109	0.6264	26.2187	105.994	54.5664
24	5.0364	-2.1864	-1.3347	3.8891	-0.4574	8.9889	-0.278	-0.1452	0.4366	-0.1936	-0.0278	0.3291	0.1375	0.2817	0.2323	0.4787	0.0011	-0.0823	0.4636	-0.0521	0.5886	16.2006	102.1076	54.5623
25	7.0105	2.6858	-0.0833	6.0862	-2.6425	1.3157	-0.3333	-0.9361	-0.0279	0.134	0.4525	0.2954	-0.1113	-1.0057	-0.3997	0.495	0.1426	-0.0211	0.7562	-0.0865	0.4671	15.3719	99.8754	62.585
26	3.3764	4.5976	-3.3027	7.1747	-2.9163	4.926	-0.5262	0.9704	0.4868	0.0546	1.5965	-0.1407	0.1025	-0.6223	-1.3927	0.9372	0.1037	-0.1453	0.7927	0.1939	0.7237	6.7774	111.137	38.3102
27	2.2383	-0.8327	0.9403	2.1108	-1.4386	3.5986	-0.2517	-0.3164	0.4446	0.219	0.1812	0.1054	-0.5542	-0.2267	0.0968	0.4934	0.0856	-0.0447	0.4931	-0.1063	0.453	14.6117	96.8761	56.2431
28	4.248	2.9742	0.4751	8.9806	-1.164	3.7558	0.5465	0.4279	1.7631	1.3401	-1.2286	1.0194	1.0395	0.9541	0.2946	1.4578	0.7568	0.5755	2.4229	0.4684	1.2716	9.4523	83.6998	91.7735
29	7.5794	2.2438	-0.849	2.2546	-1.7993	2.3811	1.2048	1.0398	-0.7364	0.085	-0.3189	0.7753	1.1245	0.3883	-0.9771	0.6833	-0.0228	0.0935	0.6966	-0.0174	0.4835	15.6253	70.7844	88.5977
30	2.2395	-0.5903	-0.0686	4.0839	-0.5835	6.2486	-0.1214	-0.529	-0.0878	0.3588	0.1538	-0.0031	-0.0212	-0.3118	-0.0554	0.4213	0.0784	0.0223	0.6895	0.0492	0.3965	22.1388	77.0281	83.0698

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 27 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 28 through 37 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 38 through 62 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 63 through 110 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 111 through 159 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 160 through 174 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 19 through 38 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 39 through 79 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 103 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 104 through 131 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 132 through 168 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 169 through 200 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 201 through 221 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 222 through 236 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 237 through 271 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 3 through 14 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 15 through 27 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 28 through 37 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 38 through 62 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 63 through 95 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 96 through 110 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 111 through 126 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 127 through 144 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 145 through 159 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 160 through 175 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 18 through 103 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 104 through 117 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 118 through 131 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 132 through 271 )

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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

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-Protein , 2 types, 4 molecules ACBD

-Non-polymers , 4 types, 46 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

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+About Yorodumi

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-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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Downloads & links

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Download

-
Validation report

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Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 4 molecules ACBD

-
Non-polymers , 4 types, 46 molecules

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Experimental details

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Experiment

-
Sample preparation

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Data collection

-
Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi