PDB-6t5a: Crystal structure of herpes simplex virus 1 pUL7:pUL51 complex

ID or keywords:

Entry

Database: PDB / ID: 6t5a

Title

Crystal structure of herpes simplex virus 1 pUL7:pUL51 complex

Components

Cytoplasmic envelopment protein 1
Tegument protein UL51

Keywords

VIRAL PROTEIN / CUSTARD / assembly / tegument / HSV-1

Function / homology

Function and homology information

viral tegument / host cell Golgi apparatus / cytoplasm
Similarity search - Function

Biological species

Human herpesvirus 1 (Herpes simplex virus type 1)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.83 Å

Authors

Butt, B.G. / Graham, S.C.

Funding support

United Kingdom, 1items

Citation

Journal: Elife / Year: 2020
Title: Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex.
Authors: Butt, B.G. / Owen, D.J. / Jeffries, C.M. / Ivanova, L. / Hill, C.H. / Houghton, J.W. / Ahmed, M.F. / Antrobus, R. / Svergun, D.I. / Welch, J.J. / Crump, C.M. / Graham, S.C.

History

Deposition	Oct 15, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 20, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 15, 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

-
Download

PDBx/mmCIF format	6t5a.cif.gz	608.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6t5a.ent.gz	505.8 KB	Display	PDB format
PDBx/mmJSON format	6t5a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t5/6t5a ftp://data.pdbj.org/pub/pdb/validation_reports/t5/6t5a	HTTPS FTP

-
Related structure data

Similar structure data	6nr7-d 4kh6-d 4jep-d 7bgk-d 7bc3-d 5cdc-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
Experimental dataset #1	Data reference: 10.17863/CAM.44914 / Data set type: diffraction image data / Metadata reference: 10.17863/CAM.44914
Other databases	SASBDB: SASDG371:2 heterotrimer of pUL7 and pUL51(8-142) from herpes simplex virus 1 SASBDB: SASDG472:4 heterohexamer of pUL7 and pUL51 from herpes simplex virus 1 SASBDB: SASDG571:2 heterotrimer of pUL7 and pUL51 from herpes simplex virus 1

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tegument protein UL51

B: Tegument protein UL51

C: Tegument protein UL51

D: Tegument protein UL51

E: Cytoplasmic envelopment protein 1

F: Cytoplasmic envelopment protein 1

G: Cytoplasmic envelopment protein 1

H: Cytoplasmic envelopment protein 1

hetero molecules

196 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS, light scattering, SEC-MALS

Unit cell

Length a, b, c (Å)	79.51, 106.3, 106.01
Angle α, β, γ (deg.)	90, 92.05, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Tegument protein UL51 / UL51 Mass: 14833.134 Da / Num. of mol.: 4 / Mutation: C9S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Gene: UL51, HHV1gp075, hmpv208_0053 / Plasmid: pOPC / Details (production host): Bicistronic expression plasmid / Production host: Escherichia coli (E. coli) / Variant (production host): T7 express lysY Iq / References: UniProt: D3YPL0
#2: Protein	Cytoplasmic envelopment protein 1 Mass: 33941.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Gene: UL7, HHV1gp012, hmpv205_0007, hmpv206_0007 / Plasmid: pOPC / Details (production host): Bicistronic expression plasmid / Production host: Escherichia coli (E. coli) / Variant (production host): T7 express lysY Iq / References: UniProt: A0A110B4Q7, UniProt: P10191*PLUS
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.4 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: pUL7:pUL51 complex was crystallized in sitting or hanging drops by mixing 1 uL of 5.3 mg/mL protein with 0.5 uL of 0.5 M benzamidine hydrochloride and 1 uL of reservoir solution containing 0. ...Details: pUL7:pUL51 complex was crystallized in sitting or hanging drops by mixing 1 uL of 5.3 mg/mL protein with 0.5 uL of 0.5 M benzamidine hydrochloride and 1 uL of reservoir solution containing 0.15 mM sodium citrate pH 5.5, 12% (v/v) 2-methyl-2,4-pentanediol, 0.1 M NaCl and equilibrating against 200 uL reservoirs at 16 C for at least one week.

Crystal

Density Matthews: 2.29 Å³/Da / Density % sol: 46.4 %

Crystal grow

Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pUL7:pUL51 complex was crystallized in sitting or hanging drops by mixing 1 uL of 5.3 mg/mL protein with 0.5 uL of 0.5 M benzamidine hydrochloride and 1 uL of reservoir solution containing 0. ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2018
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.83→105.9 Å / Num. obs: 154984 / % possible obs: 100 % / Redundancy: 6.5 % / B_iso Wilson estimate: 35.2 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.12 / R_pim(I) all: 0.051 / Net I/σ(I): 6.8
Reflection shell	Resolution: 1.83→1.86 Å / Redundancy: 6.5 % / R_merge(I) obs: 3.197 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7654 / CC_1/2: 0.321 / R_pim(I) all: 1.367 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
DIALS		data reduction
Aimless		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.83→26.57 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.95 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.123 / SU R_free Blow DPI: 0.114 / SU R_free Cruickshank DPI: 0.115

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	8093	-	RANDOM
R_work	0.194	-	-	-
obs	0.195	154885	100 %	-

Displacement parameters

B_iso mean: 45.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.235 Å²	0 Å²	0.5304 Å²
2-	-	-2.0871 Å²	0 Å²
3-	-	-	-0.1479 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: LAST / Resolution: 1.83→26.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11692	0	28	717	12437

Refinement TLS params.

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	0.0113	-0.0178	-0.1656	0.2464	0.2822	0.4473	-0.0494	0.0003	0.0349	0.0003	0.036	0.0199	0.0349	0.0199	0.0134	0.0408	0.0077	0.0128	0.0075	-0.0286	-0.0438	45.6577	15.9958	59.9475
2	0.2546	-0.3256	-0.5534	0.8065	1.8705	3.1206	0.0385	0.0781	-0.3111	0.0781	-0.0046	0.0677	-0.3111	0.0677	-0.0339	0.1236	-0.0259	0.0192	-0.0334	0.0114	-0.1019	55.174	4.9947	30.8259
3	0.0201	0.2885	-0.0852	0.9655	-0.6103	0.4158	-0.0418	0.0257	-0.0496	0.0257	0.0227	-0.0219	-0.0496	-0.0219	0.0191	0.0308	-0.0113	0.0096	-0.0039	0.0193	-0.0359	45.4655	51.1694	64.5283
4	0.002	0.1685	-0.0478	2.6759	-1.2525	1.113	-0.0113	0.3547	0.0575	0.3547	-0.0155	-0.018	0.0575	-0.018	0.0268	0.0884	-0.0053	-0.0045	-0.0496	-0.0249	-0.0591	54.2739	80.6968	53.9178
5	0.0006	-0.1251	0.0153	0.3494	-0.2176	0.2444	-0.0243	0.0026	0.0099	0.0026	0.0384	-0.0274	0.0099	-0.0274	-0.0142	0.0276	0.0099	-0.0072	-0.0101	0.0214	-0.0244	44.3641	11.5995	94.8958
6	0.3299	-0.4007	-0.504	4.187	-1.5309	0.3627	0.0268	-0.3437	-0.0943	-0.3437	-0.0641	-0.0206	-0.0943	-0.0206	0.0373	0.1158	-0.0059	0.0096	-0.076	-0.0328	-0.0667	52.5006	-18.1046	106.249
7	0.0425	0.0279	0.1242	0.2611	0.2368	0.423	-0.0177	0.0544	0.0201	0.0544	-0.0169	-0.0486	0.0201	-0.0486	0.0346	0.023	-0.0039	-0.0024	-0.0115	-0.0186	-0.0262	44.1983	46.5612	99.5583
8	0.1991	-0.452	-0.208	0.7189	1.8556	4.5935	-0.0414	-0.01	0.3636	-0.01	0.0184	0.0504	0.3636	0.0504	0.0229	0.1047	-0.001	0.0204	-0.0455	0.0266	-0.0892	51.5686	57.5625	129.3465
9	3.8058	-1.5712	0.7304	1.1813	-0.4556	1.2067	-0.0406	0.0637	0.0167	0.0637	-0.0254	0.1854	0.0167	0.1854	0.066	0.0199	0.0012	-0.002	-0.0198	-0.0466	-0.0762	48.958	14.3549	66.687
10	1.5369	0.3092	0.9316	1.5027	0.6142	3.1988	0.0702	0.1043	0.472	0.1043	0.0166	0.1515	0.472	0.1515	-0.0869	-0.0922	0.066	0.0059	-0.0956	-0.0092	-0.1312	62.0244	4.4662	67.0378
11	0.8029	-1.3773	-1.0735	2.4104	1.9518	1.4802	0.0074	0.0706	-0.024	0.0706	0.1221	0.212	-0.024	0.212	-0.1295	0.0218	0.0143	-0.0068	0.0289	-0.0416	-0.0985	52.4639	25.6231	81.1356
12	4.4894	-0.6642	-1.2068	0.9039	0.2425	0.8493	0.0109	-0.0313	0.0771	-0.0313	0.0224	0.0885	0.0771	0.0885	-0.0333	0.0222	0.0145	0.007	-0.0325	0.0341	-0.0612	49.0494	44.5237	62.9861
13	2.01	-1.2054	0.6288	3.5287	-0.8711	1.8691	0.227	-0.5774	0.1895	-0.5774	-0.2559	0.3053	0.1895	0.3053	0.0289	-0.1033	0.0476	0.0742	-0.0788	-0.0099	-0.1785	62.4855	44.7167	53.5945
14	0.9117	1.0709	-1.432	1.5974	-2.2376	2.0541	-0.0056	0.0494	0.0787	0.0494	-0.1382	0.0062	0.0787	0.0062	0.1438	0.0246	0.0191	0.0099	-0.0837	0.0111	0.0053	52.7033	30.2374	74.4178
15	4.4643	0.5864	2.0803	1.2094	0.5429	1.5059	-0.0234	0.0307	-0.0451	0.0307	0.0433	0.1543	-0.0451	0.1543	-0.0199	0.0208	-0.0112	0.0138	-0.0314	0.046	-0.0761	47.82	18.088	96.8237
16	1.5829	0.5942	-0.0809	2.2239	-0.3612	1.2976	0.0387	0.3227	-0.062	0.3227	-0.0628	0.1036	-0.062	0.1036	0.0241	-0.0658	0.006	-0.0401	-0.091	0.0156	-0.1132	60.3605	18.0011	107.2018
17	-0.0368	-0.2666	0.4819	1.1504	-1.8539	1.7728	0.0311	-0.0225	-0.0013	-0.0225	-0.1697	0.0679	-0.0013	0.0679	0.1385	0.0065	-0.0044	-0.0166	-0.0529	0.0266	-0.0131	52.3335	32.4088	85.7455
18	4.7574	1.7064	-0.8374	1.1587	-0.4723	1.1855	-0.0295	-0.0684	-0.0069	-0.0684	-0.0384	0.1285	-0.0069	0.1285	0.0679	0.0362	0.0091	0.0133	-0.0646	-0.0258	-0.0461	47.9314	48.2016	93.0484
19	1.6462	0.0405	-0.8247	1.2491	0.2452	2.8854	0.0545	-0.0075	-0.3745	-0.0075	0.0088	0.1803	-0.3745	0.1803	-0.0633	-0.0831	-0.0535	-0.0155	-0.1048	-0.0013	-0.1111	60.9927	58.0906	93.7225
20	0.6511	1.0275	0.9188	1.6096	1.7846	1.1219	0.0164	-0.0052	0.0246	-0.0052	0.1035	0.1303	0.0246	0.1303	-0.1199	0.0181	-0.0217	0.0151	0.0173	-0.0269	-0.0756	52.4879	36.9784	78.9087

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|1 - A\|90 }
2	X-RAY DIFFRACTION	2	{ A\|91 - A\|140 }
3	X-RAY DIFFRACTION	3	{ B\|1 - B\|90 }
4	X-RAY DIFFRACTION	4	{ B\|91 - B\|140 }
5	X-RAY DIFFRACTION	5	{ C\|1 - C\|90 }
6	X-RAY DIFFRACTION	6	{ C\|91 - C\|140 }
7	X-RAY DIFFRACTION	7	{ D\|1 - D\|90 }
8	X-RAY DIFFRACTION	8	{ D\|91 - D\|140 }
9	X-RAY DIFFRACTION	9	{ E\|1 - E\|50 }
10	X-RAY DIFFRACTION	10	{ E\|51 - E\|281 }
11	X-RAY DIFFRACTION	11	{ E\|282 - E\|999 }
12	X-RAY DIFFRACTION	12	{ F\|1 - F\|50 }
13	X-RAY DIFFRACTION	13	{ F\|51 - F\|281 }
14	X-RAY DIFFRACTION	14	{ F\|282 - F\|999 }
15	X-RAY DIFFRACTION	15	{ G\|1 - G\|50 }
16	X-RAY DIFFRACTION	16	{ G\|51 - G\|281 }
17	X-RAY DIFFRACTION	17	{ G\|282 - G\|999 }
18	X-RAY DIFFRACTION	18	{ H\|1 - H\|50 }
19	X-RAY DIFFRACTION	19	{ H\|51 - H\|281 }
20	X-RAY DIFFRACTION	20	{ H\|282 - H\|999 }

-
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://pdbjlc1.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