8SGN: Epstein-Barr virus glycoprotein 350

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. Determined by X-ray diffraction at 2.2 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Macaca fascicularis, Human herpesvirus 4
Chains: 3
Atoms: 6,884
Mol. weight: 97.43 kDa
Ligands: NAG
Released: 17 Apr 2024

Explore 8SGN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SGN contains 27 α-helices and 78 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain G: 9 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	11
β-strand	18-19	2	12
β-strand	25-30	6	13
β-strand	44-54	11	11
β-strand	57-68	12	11
β-strand	75-76	2	13
β-strand	81-82	2	11
α-helix	84-85	2
α-helix	88-91	4
β-strand	92-98	7	13
β-strand	101-107	7	13
β-strand	123-133	11	11
β-strand	139-146	8	11
β-strand	151-152	2	11
β-strand	166-175	10	14
β-strand	178-180	3	14
β-strand	181-187	7	15
β-strand	195-204	10	14
β-strand	207-212	6	14
β-strand	220	1	14
β-strand	224-229	6	15
β-strand	231-232	2	14
β-strand	234-235	2	12
α-helix	236-237	2
α-helix	240-241	2
β-strand	242-247	6	15
α-helix	248-249	2
β-strand	260-267	8	15
α-helix	273-275	3
β-strand	279-288	10	14
β-strand	297-305	9	14
α-helix	315-316	2
β-strand	317-324	8	16
β-strand	325	1	17
β-strand	328	1	17
β-strand	329-333	5	18
α-helix	334-336	3
β-strand	346-352	7	16
β-strand	364-366	3	16
β-strand	379-383	5	18
α-helix	384	1
β-strand	389-393	5	18
β-strand	401-409	9	16
β-strand	415-423	9	16

Chain H: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	33-39	7	8
β-strand	46-52	7	8
β-strand	56-59	4	8
α-helix	64-66	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-96	9	8
α-helix	98-100	3
β-strand	100B-103	5	8
β-strand	107-109	3	8
β-strand	110-111	2	7
α-helix	115-116	2
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	135-145	11	9
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	186-191	6
β-strand	194-200	7	10
α-helix	201-203	3
β-strand	205-211	7	10

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	5	1	2
β-strand	9-13	4	1
β-strand	19-24	6	2
β-strand	33-38	6	1
β-strand	45-48	4	1
β-strand	49	1	3
β-strand	53	1	3
α-helix	54-55	2
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	85-91	7	1
β-strand	96-99	4	1
β-strand	102-106	5	1
α-helix	109-111	3
α-helix	113-114	2
β-strand	115-119	5	4
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	4
β-strand	146-151	6	5
β-strand	154-156	3	5
β-strand	160-162	3	4
α-helix	163-165	3
β-strand	166-167	2	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	192-198	7	5
β-strand	201-207	7	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cy651H02 Fab light chain	L	protein	214	Macaca fascicularis
Cy651H02 Fab heavy chain	H	protein	223	Macaca fascicularis
Envelope glycoprotein gp350	G	protein	431	Human herpesvirus 4	P03200 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8SGN_1 Cy651H02 Fab light chain (chains L)
QAALTQPPSVSGSPGQSVTISCTGTSSDIGGYNYVSWYQQHPGKAPKVMIYEVSKRPSGV
SDRFSGSKSGNIASLTISGLQAEDEADYYCSSYAGSNTFLFGGGTRLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVEVAWKADGSAVNAGVETTKPSKQSNNKYAASS
YLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPAE

Sequence of entity 2 (H), FASTA

>8SGN_2 Cy651H02 Fab heavy chain (chains H)
QLQLQESGPGVVKPSETLSLTCTISGGSFSTYYWTWIRQPPGKGLEWVGYIGNGGRSLNY
NPSLKSRITLSVDASKNQFSLKVTSVTAADTAVYYCGRARGLRGNWFDVWGPGVLVTVSS
ASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTC

Sequence of entity 3 (G), FASTA

>8SGN_3 Envelope glycoprotein gp350 (chains G)
MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQ
LDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEE
QQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLD
VTLPLSLPTSAQDSNFSVKTEMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVP
SGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQ
SNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTET
DFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVI
FSKAPHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Water and common crystallization additives (EDO, TRS) are not listed.

Primary citation

Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350. Joyce, M.G., Bu, W., Chen, W.H. et al. Immunity (2025) 58:295. DOI 10.1016/j.immuni.2025.01.010 · PubMed

Other PDB entries of the same protein (UniProt P03200 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SM0 1.68 Å, Crystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr…
8SIC 2.76 Å, Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with…
9MA7 3.14 Å, Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5…
8SM1 3.29 Å, Crystal structure of human antibody 769A9 in complex with epstein-barr virus major…
9MA0 3.33 Å, Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11

Browse structure collections

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