8SIC: Epstein-Barr virus glycoprotein 350

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine. Determined by X-ray diffraction at 2.76 Å resolution. Released 17 Apr 2024.

Method: X-ray diffraction
Resolution: 2.76 Å
Organisms: Macaca fascicularis, Human herpesvirus 4
Chains: 6
Atoms: 13,230
Mol. weight: 190.91 kDa
Ligands: NAG, ZN
Released: 17 Apr 2024

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

Secondary structure: helices and β-sheets

8SIC contains 41 α-helices and 156 β-strands across 6 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 A: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	33-39	7	3
β-strand	46-52	7	3
β-strand	57-59	3	3
β-strand	67-72	6	1
α-helix	74-76	3
β-strand	77-82	6	1
β-strand	88-95	8	3
β-strand	103	1	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	115-116	2
β-strand	120-124	5	4
α-helix	127-129	3
β-strand	135-145	11	4
β-strand	151-154	4	5
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain B: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	6
β-strand	5	1	7
β-strand	9-13	4	8
β-strand	19-24	6	7
β-strand	33-38	6	8
β-strand	45-48	4	8
β-strand	49	1	9
β-strand	53	1	9
β-strand	56	1	10
β-strand	58	1	10
β-strand	62-65	4	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-92	8	8
β-strand	95B-98	4	8
β-strand	99	1	6
β-strand	102-106	5	8
α-helix	108-110	3
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	11
β-strand	145-150	6	12
β-strand	154	1	12
β-strand	159-161	3	11
α-helix	162-164	3
β-strand	165-166	2	11
β-strand	172-180	9	11
α-helix	182-187	6
β-strand	191-197	7	12
β-strand	200-206	7	12

Chain E: 4 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	13
β-strand	19	1	14
β-strand	25-30	6	15
β-strand	44-53	10	13
β-strand	58-68	11	13
β-strand	75-76	2	15
β-strand	80-81	2	13
α-helix	89-91	3
β-strand	92-98	7	15
β-strand	101-107	7	15
β-strand	123	1	16
β-strand	124-133	10	13
β-strand	139-146	8	13
β-strand	152	1	16
β-strand	166-167	2	17
β-strand	172-175	4	18
β-strand	178-180	3	18
β-strand	181-183	3	19
β-strand	197-204	8	17
β-strand	207-213	7	17
β-strand	226-229	4	19
β-strand	230-232	3	17
β-strand	234	1	14
β-strand	242-245	4	19
β-strand	264-267	4	19
α-helix	273-275	3
β-strand	280-286	7	17
β-strand	296-302	7	17
β-strand	303-305	3	18
α-helix	315-316	2
β-strand	318-324	7	20
β-strand	330-333	4	21
β-strand	346-352	7	20
β-strand	365-367	3	20
β-strand	380-383	4	21
α-helix	385-387	3
β-strand	389-392	4	21
β-strand	394	1	22
β-strand	396	1	22
β-strand	401-409	9	20
β-strand	412-423	12	20

Chain G: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	10-16	7	23
β-strand	18-19	2	24
β-strand	25-30	6	25
β-strand	44-54	11	23
β-strand	57-68	12	23
β-strand	75-76	2	25
β-strand	80-82	3	23
α-helix	88-91	4
β-strand	92-98	7	25
β-strand	101-107	7	25
β-strand	124-133	10	23
β-strand	139-151	13	23
α-helix	152	1
α-helix	157-160	4
β-strand	163	1	26
β-strand	166-167	2	27
α-helix	170-171	2
β-strand	172-175	4	27
β-strand	178-180	3	27
β-strand	181-187	7	28
β-strand	197-204	8	27
β-strand	207-213	7	27
β-strand	224-229	6	28
β-strand	230-232	3	27
β-strand	234-235	2	24
α-helix	236-237	2
β-strand	242-247	6	28
β-strand	260-267	8	28
α-helix	273-275	3
β-strand	279-286	8	27
β-strand	297-305	9	27
α-helix	315-316	2
β-strand	318-324	7	29
β-strand	328-333	6	30
α-helix	334-336	3
β-strand	346-352	7	29
α-helix	358-361	4
β-strand	364-367	4	29
β-strand	379-383	5	30
α-helix	388	1
β-strand	389-394	6	30
β-strand	401-409	9	29
β-strand	414-423	10	29

Chain H: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	11-12	2	32
β-strand	18-25	8	31
β-strand	33-39	7	26
β-strand	46-51	6	26
β-strand	57-59	3	26
β-strand	67-72	6	31
α-helix	73-75	3
β-strand	77-82	6	31
α-helix	84-86	3
β-strand	88-95	8	26
β-strand	103	1	26
β-strand	107-109	3	26
β-strand	110-111	2	32
α-helix	115-116	2
β-strand	120-124	5	33
β-strand	135-145	11	33
β-strand	151-154	4	34
α-helix	155-157	3
β-strand	163-165	3	33
α-helix	166-168	3
β-strand	169-170	2	33
β-strand	176-185	10	33
α-helix	189-191	3
β-strand	195-200	6	34
α-helix	201-203	3
β-strand	205-210	6	34
α-helix	211	1

Chain L: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	35
β-strand	9-13	4	36
β-strand	19-24	6	35
β-strand	33-38	6	36
β-strand	45-48	4	36
β-strand	49	1	37
β-strand	53	1	37
β-strand	62-65	4	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	85-92	8	36
β-strand	95B-98	4	36
β-strand	102-106	5	36
α-helix	108-110	3
α-helix	112-113	2
β-strand	114-118	5	38
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	38
β-strand	145-150	6	39
β-strand	154-155	2	39
α-helix	161-164	4
β-strand	165-166	2	38
β-strand	172-181	10	38
α-helix	182-187	6
β-strand	191-197	7	39
β-strand	200-206	7	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cy137C02 Fab heavy chain	A, H	protein	222	Macaca fascicularis
Cy137C02 Fab light chain	B, L	protein	215	Macaca fascicularis
Envelope glycoprotein gp350	E, G	protein	431	Human herpesvirus 4	P03200 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>8SIC_1 Cy137C02 Fab heavy chain (chains A, H)
QLQLQESGPGLVKPSETLSLTCAVSGGSISGYYWSWIRQPPGKGPEWIGFIDGNTVGTNY
NPSLKSRVTLSKDTSKNQFSLKVSSVTAADTAVYYCARKPLRRYFWFDVWGPGVLVTVSS
ASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEIKT

Sequence of entity 2 (B, L), FASTA

>8SIC_2 Cy137C02 Fab light chain (chains B, L)
QSVLTQPPSVSGDPGQRVTISCTGSSSNIGAGYYVYWYQQFPGTAPKLLIYQDNKRPSGV
SDRFSGSKSGTSASLTITGLQPGDEADYYCSAWDSSLSAVMFGRGTRLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVEVAWKADGSAVNAGVETTKPSKQSNNKYAAS
SYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPAE

Sequence of entity 3 (E, G), FASTA

>8SIC_3 Envelope glycoprotein gp350 (chains E, 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	17
ZN	Zinc ion	Zn	2

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…
8SGN 2.2 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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