9MA0: EBV gp350 D123

Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11. Determined by electron microscopy at 3.33 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 3.33 Å
Organisms: Human herpesvirus 4 strain B95-8, Homo sapiens
Chains: 3
Atoms: 4,989
Mol. weight: 103.6 kDa
Released: 18 Mar 2026

Explore 9MA0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MA0 contains 6 α-helices and 60 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 A: 2 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	10	1	2
β-strand	16-21	6	3
β-strand	38-44	7	1
β-strand	49-55	7	1
β-strand	67	1	3
β-strand	83-89	7	3
β-strand	92-98	7	3
β-strand	114-124	11	1
β-strand	130-143	14	1
β-strand	163-165	3	4
β-strand	170-171	2	4
β-strand	172-178	7	5
β-strand	186	1	6
β-strand	188-194	7	4
β-strand	199-203	5	4
β-strand	216-220	5	5
β-strand	222-223	2	4
β-strand	225	1	2
β-strand	233-238	6	5
β-strand	251-258	8	5
β-strand	270-271	2	4
β-strand	274-277	4	4
β-strand	279	1	6
β-strand	288-290	3	4
β-strand	293-296	4	4
α-helix	306-307	2
β-strand	310-314	5	7
β-strand	316	1	8
β-strand	319-324	6	8
β-strand	338-343	6	7
β-strand	357-358	2	7
α-helix	363-364	2
β-strand	370-373	4	8
β-strand	380-385	6	8
β-strand	394-398	5	7
β-strand	406-413	8	7

Chain B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	9
β-strand	10-11	2	10
β-strand	18-23	6	9
α-helix	30-32	3
β-strand	37-38	2	11
β-strand	39	1	12
β-strand	41	1	13
β-strand	43	1	13
β-strand	46-47	2	11
α-helix	70-72	3
β-strand	80-85	6	9
β-strand	93	1	12
β-strand	100	1	14
β-strand	111	1	14
α-helix	112-113	2
β-strand	121	1	12
β-strand	122-123	2	10

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	10	1	15
β-strand	13	1	16
β-strand	19	1	17
β-strand	39-43	5	15
β-strand	49-51	3	15
β-strand	67	1	17
β-strand	80	1	17
β-strand	89-94	6	15
β-strand	103	1	15
β-strand	107-109	3	15
β-strand	111	1	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein GP350	A	protein	478	Human herpesvirus 4 strain B95-8	P03200 (AlphaFold model)
4A11 heavy chain	B	protein	248	Homo sapiens
4A11 light chain	C	protein	237	Homo sapiens

Sequence of entity 1 (A), FASTA

>9MA0_1 Envelope glycoprotein GP350 (chains A)
MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQ
LDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEE
QQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLD
VTLPLSLPTSAQDSNFSVKTQMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVP
SGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQ
SNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTET
DFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVI
FSKAPESTTTSPTLNTTGFADPNTTTGLPSSTHVPTNLTAPASTGPTVSTGSHHHHHH

Sequence of entity 2 (B), FASTA

>9MA0_2 4A11 heavy chain (chains B)
MGWSCIILFLVATATGVHSQVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYIHWVRQAP
GQGLEWMGWMNPNSGATNYAQKFQGRVTMTRDTSINTAYMELSSLRSDDTAVYFCAKDPR
YSSSWRHNWFDPWGQGTLVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKR
VEPKSCDK

Sequence of entity 3 (C), FASTA

>9MA0_3 4A11 light chain (chains C)
MGWSCIILFLVATATGSWADIVLTQSPLSLTVTPGEPASISCRSSQSLLHSSGHNFLSWY
LQKPGQSPQLLIYLGSNRASGVPDRFSGSGTGADFTLKISRVEAEDVGVYYCLQTLRAPF
TFGQGTRLEIKGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPV
KAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11. Ma, H.Y., Sun, C. To be published.

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…
8SM1 3.29 Å, Crystal structure of human antibody 769A9 in complex with epstein-barr virus major…

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