PDB-2giy: Crystal Structure of the C-terminal domain of the HSV-1 gE ectodomain

ID or keywords:

Entry

Database: PDB / ID: 2giy

Title

Crystal Structure of the C-terminal domain of the HSV-1 gE ectodomain

Components

Glycoprotein E

Keywords

VIRAL PROTEIN / viral Fc receptor / Ig V domain

Function / homology

Function and homology information

host cell junction / host cell Golgi membrane / host cell endosome membrane / cell junction / host cell Golgi apparatus / membrane => GO:0016020 / virus-mediated perturbation of host defense response / viral envelope / virion membrane / identical protein binding / membrane
Similarity search - Function

Biological species

Human herpesvirus 1 (Herpes simplex virus type 1)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.78 Å

Authors

Sprague, E.R. / Wang, C. / Baker, D. / Bjorkman, P.J.

Citation

Journal: Plos Biol. / Year: 2006
Title: Crystal Structure of the HSV-1 Fc Receptor Bound to Fc Reveals a Mechanism for Antibody Bipolar Bridging.
Authors: Sprague, E.R. / Wang, C. / Baker, D. / Bjorkman, P.J.

History

Deposition	Mar 29, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2giy.cif.gz	84.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2giy.ent.gz	66.1 KB	Display	PDB format
PDBx/mmJSON format	2giy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2giy_validation.pdf.gz	438.1 KB	Display	wwPDB validaton report
Full document	2giy_full_validation.pdf.gz	443.8 KB	Display
Data in XML	2giy_validation.xml.gz	18 KB	Display
Data in CIF	2giy_validation.cif.gz	25.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gi/2giy ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2giy	HTTPS FTP

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Related structure data

Related structure data	2gj7C 2gjy C: citing same article (ref.)
Similar structure data	4qq7-d 5hft-2 6hdt-d 3pvp-d 3mxi-d 3may-2 2pjl-d 7a79-d 6m1x-2 4kbg-2 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: Glycoprotein E

B: Glycoprotein E

42.3 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)	45.681, 91.242, 47.409
Angle α, β, γ (deg.)	90.00, 117.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

The biological assembly is one monomer of CgE in the asymmetric unit

#1: Protein	Glycoprotein E Mass: 21142.627 Da / Num. of mol.: 2 / Fragment: C-terminal domain of the gE ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1) Genus: Simplexvirus / Strain: KOS / Gene: GE, US8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04488, UniProt: Q703E9*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Glycoprotein E

Mass: 21142.627 Da / Num. of mol.: 2 / Fragment: C-terminal domain of the gE ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Strain: KOS / Gene: GE, US8 / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: P04488, UniProt: Q703E9*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.07 Å³/Da / Density % sol: 40.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 28-32% (w/v) PEG 4000, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL9-1	1	0.97011
SYNCHROTRON	SSRL	BL9-2	2	0.9787, 0.9050, 0.9795

Detector

Type	ID	Detector	Date
MAR scanner 345 mm plate	1	IMAGE PLATE	Nov 24, 2001
ADSC QUANTUM 4	2	CCD	Mar 22, 2001

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MIRRORS	SINGLE WAVELENGTH	M	x-ray	1
2	MIRRORS	MAD	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97011	1
2	0.9787	1
3	0.905	1
4	0.9795	1

Reflection

Χ²: 1.04 / D res high: 2 Å / D res low: 99 Å / Redundancy: 5 %

ID	Av σ(I) over netI	Number	R_merge(I) obs	Num. obs	% possible obs
1	28.4	83423	0.043	22997	99.4
2	26.7	83148	0.042	22906	99.4
3	27.2	82692	0.042	22911	99.5

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.43	99	1170	97.7	1	0.025	1.03	5
4.31	5.43	1151	99.3	1	0.022	1.031	5
3.76	4.31	1177	99.8	1	0.024	1.036	5.1
3.42	3.76	1149	99.7	1	0.029	1.022	5.1
3.17	3.42	1155	99.7	1	0.036	1.042	5.1
2.99	3.17	1157	99.9	1	0.044	1.053	5.1
2.84	2.99	1151	99.9	1	0.048	1.024	5.1
2.71	2.84	1153	99.9	1	0.056	1.007	5.1
2.61	2.71	1158	99.9	1	0.07	1.036	5
2.52	2.61	1135	99.8	1	0.08	1.046	5.1
2.44	2.52	1159	99.7	1	0.082	1.065	5.1
2.37	2.44	1144	99.7	1	0.096	1.065	5.1
2.31	2.37	1150	99.7	1	0.112	1.018	5
2.25	2.31	1146	99.6	1	0.125	1.061	5
2.2	2.25	1147	99.7	1	0.138	1.061	5
2.15	2.2	1128	99.3	1	0.144	1.064	5
2.11	2.15	1166	98.5	1	0.172	1.044	5
2.07	2.11	1110	98.8	1	0.199	1.062	5
2.03	2.07	1140	99.1	1	0.24	1.059	5
2	2.03	1151	99.1	1	0.258	1.075	4.2
5.43	99	1166	97.7	2	0.019	1.037	5
4.31	5.43	1148	99.2	2	0.018	1.03	5
3.76	4.31	1163	99.7	2	0.022	1.043	5.1
3.42	3.76	1148	99.8	2	0.027	1.026	5.1
3.17	3.42	1152	99.8	2	0.034	1.005	5.1
2.99	3.17	1143	99.9	2	0.043	1.087	5.1
2.84	2.99	1156	99.9	2	0.05	1.041	5.1
2.71	2.84	1156	99.9	2	0.059	1.058	5.1
2.61	2.71	1147	99.9	2	0.073	1.03	5
2.52	2.61	1128	99.8	2	0.084	1.022	5.1
2.44	2.52	1167	99.7	2	0.095	1.014	5.1
2.37	2.44	1132	99.7	2	0.104	1.037	5.1
2.31	2.37	1133	99.6	2	0.127	1.004	5
2.25	2.31	1140	99.7	2	0.145	1.037	5
2.2	2.25	1172	99.7	2	0.162	1.057	5
2.15	2.2	1118	99.1	2	0.167	1.051	5
2.11	2.15	1145	98.4	2	0.198	1.014	5
2.07	2.11	1116	99.1	2	0.236	1.022	5
2.03	2.07	1126	98.8	2	0.276	1.052	5
2	2.03	1150	98.5	2	0.288	1.053	4.2
5.43	99	1163	97.5	3	0.021	1.012	5
4.31	5.43	1147	99.3	3	0.019	1.038	5
3.76	4.31	1163	99.8	3	0.022	1.056	5.1
3.42	3.76	1147	99.7	3	0.027	1.032	5.1
3.17	3.42	1148	99.8	3	0.034	1.054	5.1
2.99	3.17	1145	99.9	3	0.041	1.033	5.1
2.84	2.99	1148	99.8	3	0.049	1.049	5.1
2.71	2.84	1160	99.9	3	0.058	1.063	5.1
2.61	2.71	1143	99.9	3	0.074	1.038	5
2.52	2.61	1131	99.9	3	0.082	1.004	5.1
2.44	2.52	1161	99.6	3	0.088	1.023	5.1
2.37	2.44	1137	99.9	3	0.098	1.05	5.1
2.31	2.37	1137	99.7	3	0.114	1.054	5
2.25	2.31	1137	99.8	3	0.129	1.084	5
2.2	2.25	1156	98.8	3	0.145	1.007	5
2.15	2.2	1120	99.7	3	0.142	1.012	5
2.11	2.15	1169	99.7	3	0.169	1.076	5
2.07	2.11	1118	99.5	3	0.195	1.014	5
2.03	2.07	1123	98.9	3	0.245	1.081	5
2	2.03	1158	99.1	3	0.266	1.073	4.2

Reflection

Resolution: 1.78→99 Å / Num. all: 32765 / Num. obs: 32765 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5 % / R_merge(I) obs: 0.082 / Χ²: 1.049 / Net I/σ(I): 16.1

Reflection shell

Resolution: 1.78→1.81 Å / % possible obs: 72.6 % / Redundancy: 4.2 % / R_merge(I) obs: 0.331 / Num. unique obs: 1203 / Χ²: 1.071 / % possible all: 72.6

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 2 Å / D res low: 30 Å / FOM : 0.36 / Reflection: 22879

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9788	4.29	-6.26
1	3 wavelength	2	0.905	3.28	-1.55
1	3 wavelength	3	0.9795	2.37	-10.13

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	60	0.719	0.496	0.273	0.599
2	Se	57.701	0.728	0.677	0.281	0.512
3	Se	21.768	0.703	0.469	0.487	0.353
4	Se	31.739	0.489	0.699	0.265	0.418
5	Se	19.914	0.847	0.227	0.437	0.175
6	Se	3.751	0.717	0.859	0.26	0.175
7	Se	46.296	0.513	0.945	0.157	0.401

Phasing MAD shell

Resolution (Å)	FOM	Reflection
7.17-30	0.7	1073
4.53-7.17	0.65	1867
3.55-4.53	0.57	2414
3.01-3.55	0.48	2827
2.66-3.01	0.4	3198
2.41-2.66	0.29	3543
2.22-2.41	0.19	3852
2.06-2.22	0.14	4105

Phasing dm

FOM : 0.51 / FOM acentric: 0.51 / FOM centric: 0.51 / Reflection: 22753 / Reflection acentric: 22076 / Reflection centric: 677

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
5.7-29.887	0.92	0.91	0.94	969	893	76
3.6-5.7	0.9	0.9	0.87	2973	2843	130
2.9-3.6	0.75	0.75	0.65	3827	3708	119
2.5-2.9	0.54	0.54	0.38	3867	3761	106
2.1-2.5	0.32	0.32	0.22	6864	6705	159
2-2.1	0.18	0.18	0.14	4253	4166	87

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.03	phasing
RESOLVE	2.03	phasing
CNS	1.1	refinement
PDB_EXTRACT	1.701	data extraction
Blu-Ice		data collection

Refinement

Method to determine structure:

MAD / Resolution: 1.78→36.47 Å / R_factor R_free error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	3213	9.8 %	random
R_work	0.198	-	-	-
all	-	32875	-	-
obs	-	32739	99.6 %	-

Solvent computation

Solvent model: CNS bulk solvent model used / B_sol: 52.0256 Å² / k_sol: 0.390878 e/Å³

Displacement parameters

B_iso max: 48.92 Å² / B_iso mean: 19.31 Å² / B_iso min: 7.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.18 Å²	0 Å²	-1.38 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	1.15 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.22 Å	0.19 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.16 Å	0.09 Å
Luzzati d res high	-	1.78

Refinement step

Cycle: LAST / Resolution: 1.78→36.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2739	0	0	275	3014

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	x_bond_d	0.007
X-RAY DIFFRACTION	x_angle_deg	1.4
X-RAY DIFFRACTION	x_torsion_deg	26.4
X-RAY DIFFRACTION	x_torsion_impr_deg	0.83

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	% reflection R_free (%)	R_factor R_work	Num. reflection R_work	R_factor R_free error	Num. reflection all	Num. reflection obs	% reflection obs (%)
1.78-1.86	0.265	385	9.7	0.223	3569	0.014	4096	3954	96.5
1.86-1.96	0.255	402	9.8	0.205	3682	0.013	4092	4084	99.8
1.96-2.08	0.234	388	9.4	0.2	3732	0.012	4127	4120	99.8
2.08-2.24	0.222	395	9.7	0.19	3682	0.011	4079	4077	100
2.24-2.47	0.232	412	10.1	0.196	3687	0.011	4103	4099	99.9
2.47-2.83	0.249	397	9.6	0.208	3725	0.012	4123	4122	100
2.83-3.56	0.217	401	9.7	0.199	3715	0.011	4117	4116	100
3.56-36.47	0.189	433	10.4	0.189	3734	0.009	4167	4167	100

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	CNS_TOPPAR:protein_rep.param	CNS_TOPPAR:protein.top
X-RAY DIFFRACTION	2	CNS_TOPPAR:dna-rna_rep.param	CNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION	3	CNS_TOPPAR:water_rep.param	CNS_TOPPAR:water.top
X-RAY DIFFRACTION	4	CNS_TOPPAR:ion.param	CNS_TOPPAR:ion.top

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