PDB-8sgn: Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) ...

ID or keywords:

Entry

Database: PDB / ID: 8sgn

Title

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine

Components

(Cy651H02 Fab ...) x 2
Envelope glycoprotein gp350

Keywords

VIRAL PROTEIN/IMMUNE SYSTEM / Epstein-Barr virus / immune system / monoclonal antibody / macaques / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

host cell membrane / virion membrane / membrane
Similarity search - Function

Biological species

Macaca fascicularis (crab-eating macaque)

Human herpesvirus 4 (Epstein-Barr virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Joyce, M.G. / Jensen, J.L. / Chen, W.H. / Kanekiyo, M.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine
Authors: Joyce, M.G. / Jensen, J.L. / Chen, W.H. / Kanekiyo, M.

History

Deposition	Apr 12, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8sgn.cif.gz	350.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8sgn.ent.gz	284.2 KB	Display	PDB format
PDBx/mmJSON format	8sgn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8sgn_validation.pdf.gz	938.4 KB	Display	wwPDB validaton report
Full document	8sgn_full_validation.pdf.gz	948.2 KB	Display
Data in XML	8sgn_validation.xml.gz	34.9 KB	Display
Data in CIF	8sgn_validation.cif.gz	49.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sg/8sgn ftp://data.pdbj.org/pub/pdb/validation_reports/sg/8sgn	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

L: Cy651H02 Fab light chain

H: Cy651H02 Fab heavy chain

G: Envelope glycoprotein gp350

hetero molecules

97.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	139.148, 139.148, 172.337
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	H-465- HOH

-
Protein , 1 types, 1 molecules G

#3: Protein	Envelope glycoprotein gp350 / Membrane antigen / MA Mass: 46895.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus) Strain: B95-8 / Gene: BLLF1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P03200

-
Antibody , 2 types, 2 molecules LH

#1: Antibody	Cy651H02 Fab light chain Mass: 22490.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca fascicularis (crab-eating macaque) Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody	Cy651H02 Fab heavy chain Mass: 23765.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca fascicularis (crab-eating macaque) Cell line (production host): Expi293 / Production host: Homo sapiens (human)

-
Sugars , 2 types, 10 molecules

#4: Polysaccharide

alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-6DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#7: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

-
Non-polymers , 3 types, 321 molecules

#5: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.48 Å³/Da / Density % sol: 64.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.72M ammonium sulfate, 0.1M Tris pH 8.0

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2016
Radiation	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. obs: 55717 / % possible obs: 88 % / Redundancy: 2.5 % / R_merge(I) obs: 0.15 / Net I/σ(I): 6.45
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 1.4 % / R_merge(I) obs: 0.368 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 1165 / % possible all: 45.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→32.92 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2366	2951	5.3 %
R_work	0.1931	-	-
obs	0.1954	55717	87.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.2→32.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6466	0	124	294	6884

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6715
X-RAY DIFFRACTION	f_angle_d	0.644	9118
X-RAY DIFFRACTION	f_dihedral_angle_d	8.953	992
X-RAY DIFFRACTION	f_chiral_restr	0.049	1065
X-RAY DIFFRACTION	f_plane_restr	0.005	1147

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 (%)
2.2-2.23	0.3247	93	0.2735	1165	X-RAY DIFFRACTION	42
2.23-2.27	0.3406	66	0.2822	1411	X-RAY DIFFRACTION	49
2.27-2.31	0.3238	94	0.2761	1592	X-RAY DIFFRACTION	56
2.31-2.36	0.3128	93	0.2729	1908	X-RAY DIFFRACTION	66
2.36-2.41	0.3148	114	0.2763	2172	X-RAY DIFFRACTION	75
2.41-2.46	0.3329	143	0.2733	2306	X-RAY DIFFRACTION	82
2.46-2.52	0.3149	181	0.2642	2509	X-RAY DIFFRACTION	90
2.52-2.58	0.2954	195	0.2519	2669	X-RAY DIFFRACTION	95
2.58-2.65	0.3185	186	0.2503	2758	X-RAY DIFFRACTION	97
2.65-2.73	0.3261	136	0.2423	2847	X-RAY DIFFRACTION	99
2.73-2.81	0.2843	170	0.2315	2854	X-RAY DIFFRACTION	100
2.81-2.91	0.2667	152	0.2284	2844	X-RAY DIFFRACTION	100
2.91-3.03	0.2494	128	0.2109	2870	X-RAY DIFFRACTION	100
3.03-3.17	0.2799	140	0.2208	2893	X-RAY DIFFRACTION	100
3.17-3.34	0.2346	122	0.2067	2869	X-RAY DIFFRACTION	100
3.34-3.54	0.2507	199	0.1893	2818	X-RAY DIFFRACTION	100
3.55-3.82	0.2597	85	0.1735	2926	X-RAY DIFFRACTION	100
3.82-4.2	0.2332	169	0.1679	2828	X-RAY DIFFRACTION	100
4.2-4.81	0.1639	196	0.1387	2818	X-RAY DIFFRACTION	100
4.81-6.05	0.1885	130	0.1602	2879	X-RAY DIFFRACTION	100
6.05-32.92	0.207	159	0.187	2830	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	3.2628	3.4426	-3.2122	8.288	0.5677	6.6936	-0.1511	0.2869	0.1118	-0.1708	0.1805	0.0247	0.0805	0.0067	0.0007	0.2003	-0.0001	-0.0319	0.3094	-0.007	0.1865	-43.9703	4.3591	40.2414
2	3.0969	0.6594	-0.9616	2.2756	-1.5582	2.8681	0.1754	-0.054	0.1886	-0.0418	-0.1301	0.2415	-0.0687	-0.343	-0.077	0.2545	0.0235	0.0064	0.32	-0.0362	0.264	-46.5358	4.7595	51.5586
3	3.6093	1.2843	-0.3412	1.1252	-0.009	0.5283	0.0511	0.0754	0.3136	0.089	-0.014	-0.0146	-0.1699	0.0362	-0.041	0.3688	0.0068	-0.0299	0.3566	-0.0334	0.2571	-27.2041	15.0012	42.2221
4	6.456	0.7216	0.0862	2.2368	0.1142	3.3854	-0.0992	0.7277	0.2834	-0.2321	0.065	-0.158	-0.3528	0.4412	0.0089	0.4137	-0.0844	-0.0148	0.4515	0.0493	0.2902	-13.2663	22.5693	30.937
5	4.5664	-0.2847	-1.3487	1.7006	0.1244	2.409	0.0284	-0.4246	-0.0425	0.2686	-0.0301	-0.1655	0.0595	0.1384	0.0266	0.2654	-0.0161	-0.0223	0.3332	-0.0081	0.2272	-27.5685	0.3891	61.2552
6	4.6251	-0.1004	-1.3587	5.4411	4.2051	5.7422	0.3517	0.1868	0.6034	-0.4204	-0.4085	0.5958	-0.9214	0.0412	0.0879	0.4442	-0.0717	-0.0123	0.438	0.0163	0.5322	-10.3873	26.4712	44.9999
7	6.5754	-1.2543	0.3541	7.5276	0.2697	6.6529	0.1488	-0.9672	0.4579	0.5792	-0.0651	-0.1153	-0.4477	-0.7039	-0.1418	0.2899	-0.0223	0.0649	0.5883	-0.0743	0.4051	-13.647	22.4217	50.5928
8	3.6823	-0.5053	-0.3931	1.4376	0.1485	1.7401	-0.2139	0.3714	-0.4296	-0.0971	-0.1129	0.4266	0.3407	-0.52	0.3268	0.4424	-0.1526	0.008	0.6312	-0.1701	0.519	-73.1961	-13.208	63.9963
9	6.8151	-1.6975	-2.2447	6.1271	2.0485	6.4465	-0.0949	0.3012	-0.2812	-0.2464	0.0625	-0.065	0.7434	-0.2905	-0.0347	0.4434	-0.1204	0.0319	0.4174	-0.1506	0.4227	-65.2131	-17.3307	64.3109
10	4.4813	-1.2545	-3.9907	3.7711	1.1989	4.0834	-0.2613	0.6082	-0.0791	-0.1562	0.089	-0.0017	0.2447	-0.2226	0.2747	0.5321	-0.1132	-0.0664	0.7742	-0.1892	0.4824	-68.7841	-11.4132	57.4139
11	7.8976	1.6271	2.0539	1.8614	0.1816	4.1357	0.1082	0.3844	-0.1129	-0.1762	-0.3566	-0.2492	0.7222	0.7061	0.1629	0.4858	0.0917	0.0931	0.4892	0.1044	0.3968	-49.1663	-8.9047	81.973
12	4.8663	0.3384	1.5801	6.0087	2.3034	8.5531	-0.1733	0.0972	0.4126	0.1924	-0.0502	0.1839	-0.7502	0.5439	0.151	0.3509	-0.0478	-0.0036	0.3578	0.0353	0.2524	-49.7051	3.7938	78.3508
13	3.2872	2.009	1.296	9.4725	4.3062	7.0375	-0.1187	-0.2328	0.0071	-0.0897	-0.1984	0.1313	-0.2204	0.4554	0.3359	0.2803	-0.0208	0.0526	0.3776	0.1166	0.1676	-50.1811	-4.3234	80.3511
14	1.5524	-1.2192	1.35	3.6077	-1.6306	3.3605	0.0468	-0.4971	-0.6298	-0.0301	0.0947	0.6516	0.3438	-0.3175	-0.102	0.4623	0.0057	0.0323	0.4485	-0.1231	0.3505	-63.274	-8.6865	81.6465
15	3.6671	-1.2883	-0.0325	4.6797	0.2845	4.3309	-0.2048	0.1685	0.0808	-0.1404	-0.0852	0.7209	0.1125	-0.8584	0.2159	0.4006	-0.0091	-0.055	0.9396	-0.1323	0.7102	-96.0378	1.754	73.1352

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 24 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 25 through 75 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 76 through 140 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 141 through 211 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 1 through 119 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 120 through 145 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 146 through 213 )
8	X-RAY DIFFRACTION	8	chain 'G' and (resid 7 through 87 )
9	X-RAY DIFFRACTION	9	chain 'G' and (resid 88 through 117 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 118 through 156 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 157 through 187 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 188 through 259 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 260 through 296 )
14	X-RAY DIFFRACTION	14	chain 'G' and (resid 297 through 317 )
15	X-RAY DIFFRACTION	15	chain 'G' and (resid 318 through 424 )

-
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://pdbjlvh1.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

-
Protein , 1 types, 1 molecules G

-
Antibody , 2 types, 2 molecules LH

-
Sugars , 2 types, 10 molecules

-
Non-polymers , 3 types, 321 molecules

-
Details

-
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

-Protein , 1 types, 1 molecules G

-Antibody , 2 types, 2 molecules LH

-Sugars , 2 types, 10 molecules

-Non-polymers , 3 types, 321 molecules

-Details

-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

-
Protein , 1 types, 1 molecules G

-
Antibody , 2 types, 2 molecules LH

-
Sugars , 2 types, 10 molecules

-
Non-polymers , 3 types, 321 molecules

-
Details

-
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