PDB-4yxp: The structure of the folded domain of the signature multifunction...

ID or keywords:

Entry

Database: PDB / ID: 4yxp

Title

The structure of the folded domain of the signature multifunctional protein ICP27 from herpes simplex virus-1 reveals an intertwined dimer.

Components

mRNA export factor

Keywords

VIRAL PROTEIN / ICP27 / Herpes Simplex virus-1

Function / homology

Function and homology information

symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated suppression of host mRNA processing / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell cytoplasm / symbiont-mediated suppression of host gene expression / regulation of DNA-templated transcription / host cell nucleus / RNA binding / zinc ion binding
Similarity search - Function

Biological species

Human herpesvirus 1 (Herpes simplex virus type 1)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.92 Å

Authors

Tunnicliffe, R.B. / Schacht, M. / Levy, C.W. / Jowitt, T.A. / Sandri-Goldin, R.M. / Golovanov, A.P.

Funding support

United States, 1items

Citation

Journal: Sci Rep / Year: 2015
Title: The structure of the folded domain from the signature multifunctional protein ICP27 from herpes simplex virus-1 reveals an intertwined dimer.
Authors: Tunnicliffe, R.B. / Schacht, M. / Levy, C. / Jowitt, T.A. / Sandri-Goldin, R.M. / Golovanov, A.P.

History

Deposition	Mar 23, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 17, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4yxp.cif.gz	224.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4yxp.ent.gz	181.7 KB	Display	PDB format
PDBx/mmJSON format	4yxp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Similar structure data	5bqk-1 5bqk-2 4xea-d 2z93-2 5g60-4 5g62-1 5g60-1 4hes-3 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: mRNA export factor

B: mRNA export factor

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	99.330, 133.620, 44.970
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	mRNA export factor / Multifunctional viral protein / Immediate-early protein IE63 / Infected cell protein 27 / ICP27 / VMW63 Mass: 30098.523 Da / Num. of mol.: 2 / Fragment: UNP residues 241-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL54 / Production host: Escherichia coli (E. coli) / References: UniProt: P10238
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.48 Å³/Da / Density % sol: 50.38 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystals grown from reservoir solutions consisting of 0.09 M (NaF, NaBr, NaI), 0.1 M (Imidazole, MES) buffer system pH 6.5, 30% (Ethylene glycol, PEG 8K) [Morpheus HT96 B2 Molecular ...Details: Crystals grown from reservoir solutions consisting of 0.09 M (NaF, NaBr, NaI), 0.1 M (Imidazole, MES) buffer system pH 6.5, 30% (Ethylene glycol, PEG 8K) [Morpheus HT96 B2 Molecular Dimensions] and 0.12 M (1,6-Hexanediol, 1-Butanol 1,2-Propanediol (racemic), 2-Propanol, 1,4-Butanediol, 1,3-Propanediol), 0.1 M (Imidazole, MES) buffer system pH 6.5, 30% (Ethylene glycol, PEG 8K) [Morpheus HT96 D2 Molecular Dimensions] Temp details: Cold Room

Crystal

Density Matthews: 2.48 Å³/Da / Density % sol: 50.38 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystals grown from reservoir solutions consisting of 0.09 M (NaF, NaBr, NaI), 0.1 M (Imidazole, MES) buffer system pH 6.5, 30% (Ethylene glycol, PEG 8K) [Morpheus HT96 B2 Molecular ...
Temp details: Cold Room

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.92→46.553 Å / Num. all: 46524 / Num. obs: 46524 / % possible obs: 100 % / Redundancy: 6.6 % / R_merge(I) obs: 0.061 / Net I/σ(I): 19.02
Reflection shell	Resolution: 1.92→1.989 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 2.86 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	dev_1977	refinement
xia2		data reduction
xia2		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.92→46.553 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2026	2280	4.9 %	Random Selection
R_work	0.1682	-	-	-
obs	0.1699	46518	99.69 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.92→46.553 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4165	0	2	345	4512

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4265
X-RAY DIFFRACTION	f_angle_d	0.798	5779
X-RAY DIFFRACTION	f_dihedral_angle_d	11.37	1553
X-RAY DIFFRACTION	f_chiral_restr	0.037	649
X-RAY DIFFRACTION	f_plane_restr	0.004	755

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 (%)
1.92-1.9618	0.2979	138	0.2547	2735	X-RAY DIFFRACTION	100
1.9618-2.0074	0.2909	153	0.226	2684	X-RAY DIFFRACTION	100
2.0074-2.0576	0.2721	123	0.2121	2774	X-RAY DIFFRACTION	100
2.0576-2.1133	0.2704	137	0.2066	2698	X-RAY DIFFRACTION	100
2.1133-2.1754	0.2336	152	0.1879	2726	X-RAY DIFFRACTION	100
2.1754-2.2457	0.217	150	0.1847	2723	X-RAY DIFFRACTION	100
2.2457-2.3259	0.2064	130	0.1695	2733	X-RAY DIFFRACTION	100
2.3259-2.419	0.2029	138	0.1703	2753	X-RAY DIFFRACTION	100
2.419-2.5291	0.1902	130	0.1622	2774	X-RAY DIFFRACTION	100
2.5291-2.6624	0.2062	131	0.1683	2779	X-RAY DIFFRACTION	100
2.6624-2.8292	0.2215	156	0.1712	2760	X-RAY DIFFRACTION	100
2.8292-3.0476	0.2007	153	0.1797	2730	X-RAY DIFFRACTION	99
3.0476-3.3543	0.2158	154	0.1776	2753	X-RAY DIFFRACTION	99
3.3543-3.8394	0.2168	144	0.1648	2806	X-RAY DIFFRACTION	100
3.8394-4.8365	0.1627	144	0.1338	2831	X-RAY DIFFRACTION	100
4.8365-46.5669	0.16	147	0.1555	2979	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	2.105	0.62	0.4843	3.0266	-0.1346	1.9389	-0.0654	-0.17	0.0208	0.0994	0.0134	-0.6539	-0.0361	0.1918	0.1131	0.2058	-0.0033	-0.0321	0.3168	0.0302	0.4691	-46.9262	28.1335	27.9741
2	2.2674	-0.4295	0.4713	7.2724	-0.2145	1.5989	-0.3129	0.6927	0.0097	-0.795	0.3988	-1.0275	-0.201	0.4824	-0.0659	0.6609	-0.0287	0.2922	0.5466	-0.007	0.5839	-48.2553	18.2233	7.1205
3	4.5675	0.4846	0.7103	2.8225	0.7351	2.2932	0.2467	0.5346	-0.5822	-0.5178	0.0133	-0.5372	0.0193	0.2368	-0.2856	0.5464	0.0747	0.0496	0.3665	-0.0839	0.3037	-62.6138	-3.7543	2.8803
4	4.0338	-1.4257	1.2356	3.5722	0.0801	1.7176	0.1537	0.5185	-0.0032	-0.6186	-0.1105	-0.1888	0.3555	0.0703	-0.0457	0.5113	-0.0327	-0.0665	0.2942	-0.0219	0.2475	-75.6539	-4.5519	5.1442
5	1.37	0.1268	0.0835	2.5579	0.1199	1.0511	0.0816	-0.017	-0.2179	-0.3068	-0.0086	-0.052	0.29	-0.0143	-0.0869	0.309	-0.0237	-0.026	0.206	0.0045	0.1673	-72.7716	0.1744	14.1637
6	3.6268	-2.5187	-0.5584	5.9096	0.4319	0.4743	0.0553	-0.1963	0.2803	-0.0725	0.077	-0.1085	-0.0156	-0.0106	-0.1209	0.2108	-0.0321	-0.0223	0.2555	0.0117	0.1534	-78.6679	14.835	22.6957
7	2.9909	-0.5679	-0.6167	4.0022	0.2639	2.4793	0.0106	-0.2576	0.082	0.2417	0.0992	0.2825	0.1801	-0.1189	-0.1147	0.2299	-0.0661	0.0015	0.2812	0.0365	0.2084	-81.4533	7.0597	29.0798
8	3.5971	-0.4308	-0.6865	5.5012	-1.4208	2.7411	-0.0385	-0.3194	-0.5823	0.0269	0.1242	0.2679	0.3861	-0.1878	-0.0922	0.3645	-0.072	-0.0611	0.2833	0.0278	0.3691	-82.4547	-5.4673	22.9335
9	1.1185	0.9398	0.1527	3.0354	-0.0439	0.8024	0.0085	-0.06	0.1703	-0.1953	0.027	0.4718	-0.066	-0.1791	-0.0529	0.2371	0.0073	-0.0266	0.244	0.0164	0.2221	-80.0304	26.1862	15.4517
10	1.1631	0.3664	-0.2946	2.339	-1.4608	3.2206	0.1441	-0.0553	-0.3904	-0.2618	0.1682	0.5741	0.6534	-0.2969	-0.2772	0.2908	-0.1676	-0.0735	0.4583	0.017	0.4595	-94.4648	3.5187	21.9404
11	4.0549	1.864	1.0445	4.5162	1.1924	2.0682	-0.1683	0.1272	0.7282	-0.7053	0.0497	1.0854	-0.0527	-0.2851	0.1194	0.3647	-0.0019	-0.114	0.3415	0.0818	0.2917	-84.5507	33.0633	9.898
12	3.3079	0.0793	-0.6628	5.7549	1.5861	3.805	-0.2491	1.096	-0.0135	-1.0396	0.0421	0.0859	-0.0746	0.0197	0.0449	0.485	-0.0519	0.0645	0.3269	0.0043	0.2172	-66.9102	37.7153	7.911
13	1.7455	0.8243	0.3728	3.7454	0.1187	1.2564	-0.0728	-0.0418	0.2419	-0.0159	0.0426	-0.0029	-0.1821	-0.0191	0.0261	0.2274	-0.0004	0.0169	0.2169	-0.0061	0.2079	-67.4922	37.1773	20.953
14	1.4473	-0.2452	0.4965	3.9937	0.929	1.6058	0.047	-0.1401	-0.317	0.3483	0.0057	-0.3465	0.1989	0.0496	-0.0493	0.2004	-0.0179	0.0286	0.2686	0.0511	0.2834	-60.1381	17.8366	28.4013
15	0.5968	0.4674	0.4553	2.9666	0.5454	1.2309	0.0289	-0.0701	-0.0744	-0.0834	0.0405	-0.4416	-0.0645	0.0389	-0.0514	0.1747	-0.0091	0.0419	0.264	0.0074	0.2195	-60.6516	20.2571	21.5139

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 242 through 261 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 262 through 274 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 275 through 296 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 297 through 329 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 330 through 379 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 380 through 404 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 405 through 441 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 442 through 467 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 468 through 512 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 242 through 261 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 262 through 292 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 293 through 311 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 312 through 379 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 380 through 424 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 425 through 512 )

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