8SM1: Human antibody 769A9

Crystal structure of human antibody 769A9 in complex with epstein-barr virus major glycoprotein GP350. Determined by X-ray diffraction at 3.29 Å resolution. Released 1 May 2024.

Method: X-ray diffraction
Resolution: 3.29 Å
Organisms: Human herpesvirus 4, Homo sapiens
Chains: 3
Atoms: 6,513
Mol. weight: 96.31 kDa
Ligands: NAG
Released: 1 May 2024

Explore 8SM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SM1 contains 14 α-helices and 79 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: 6 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	11-16	6	1
β-strand	18-19	2	2
β-strand	25-30	6	3
β-strand	45-46	2	4
β-strand	48-53	6	1
β-strand	58	1	1
β-strand	61-62	2	1
β-strand	63	1	5
β-strand	66-67	2	4
β-strand	75-76	2	3
β-strand	81	1	5
β-strand	92-96	5	3
β-strand	102-107	6	3
β-strand	124-133	10	1
β-strand	139-146	8	1
α-helix	149-150	2
β-strand	151	1	1
β-strand	166-167	2	6
β-strand	172-175	4	6
β-strand	178-180	3	6
β-strand	181-187	7	7
β-strand	197-203	7	6
β-strand	208-212	5	6
β-strand	226-229	4	7
β-strand	231-232	2	6
β-strand	234-235	2	2
β-strand	242-247	6	7
α-helix	254-255	2
β-strand	260-267	8	7
α-helix	273-275	3
β-strand	279-286	8	6
β-strand	299-305	7	6
α-helix	314-316	3
β-strand	318-323	6	8
β-strand	329-333	5	9
β-strand	347-352	6	8
α-helix	358-361	4
β-strand	364-366	3	8
β-strand	379-383	5	9
β-strand	389-393	5	9
β-strand	402-408	7	8
β-strand	415-422	8	8

Chain H: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
β-strand	10-12	3	11
β-strand	15	1	12
β-strand	20	1	10
β-strand	23-25	3	10
β-strand	34-40	7	13
β-strand	44-51	8	13
β-strand	57-59	3	13
β-strand	68-72	5	10
β-strand	77-81	5	10
β-strand	82C	1	12
β-strand	89-95	7	13
β-strand	100F-103	4	13
β-strand	107-108	2	13
β-strand	109-111	3	11
α-helix	117-119	3
β-strand	120-124	5	14
β-strand	137-143	7	14
β-strand	151-154	4	15
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	177-183	7	14
β-strand	196-199	4	15

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
β-strand	10	1	17
β-strand	13	1	18
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	44-48	5	17
β-strand	54	1	17
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	85-90	6	17
β-strand	97	1	17
β-strand	102-103	2	17
β-strand	106	1	18
α-helix	112-114	3
β-strand	115-118	4	19
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	19
β-strand	144-149	6	20
β-strand	154-155	2	20
β-strand	159-164	6	19
α-helix	165-167	3
β-strand	173-182	10	19
α-helix	183-187	5
β-strand	191-198	8	20
β-strand	205-210	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp350	G	protein	431	Human herpesvirus 4	P03200 (AlphaFold model)
769A9 Fab heavy chain	H	protein	228	Homo sapiens
769A9 Fab light chain	L	protein	215	Homo sapiens

Sequence of entity 1 (G), FASTA

>8SM1_1 Envelope glycoprotein gp350 (chains G)
MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQ
LDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEE
QQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLD
VTLPLSLPTSAQDSNFSVKTEMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVP
SGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQ
SNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTET
DFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVI
FSKAPHHHHHH

Sequence of entity 2 (H), FASTA

>8SM1_2 769A9 Fab heavy chain (chains H)
QVQLVQSGAELKTPGASVKVSCKASGYTFTGYYIHWVRQAPGEGLEWTGWINPNSGATRY
GQKFQGRVTLTSDTSSSTVYMEVSNLTSDDSAVYYCARELSYSIRGTGPLGYWGLGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 3 (L), FASTA

>8SM1_3 769A9 Fab light chain (chains L)
EIVLTQSPGTLSLSPGERATLSCRASQSVASKYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQYYGSSPLTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Water and common crystallization additives (GOL) 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…
8SGN 2.2 Å, Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with…
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…
9MA0 3.33 Å, Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11

Browse structure collections

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