9MA7: EBV gp350 D123

Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9. Determined by electron microscopy at 3.14 Å resolution. Released 18 Mar 2026.

Method: Electron microscopy
Resolution: 3.14 Å
Organisms: human gammaherpesvirus 4, Homo sapiens
Chains: 7
Atoms: 8,435
Mol. weight: 204.86 kDa
Released: 18 Mar 2026

Explore 9MA7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MA7 contains 19 α-helices and 112 β-strands across 7 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: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	9-10	2	2
β-strand	16-20	5	3
β-strand	35-45	11	1
β-strand	48-59	12	1
β-strand	66-67	2	3
β-strand	71-73	3	1
β-strand	75	1	4
α-helix	79-82	4
β-strand	83-89	7	3
β-strand	92-98	7	3
β-strand	104	1	4
β-strand	114-124	11	1
β-strand	130-143	14	1
α-helix	148-150	3
β-strand	157	1	5
β-strand	162-166	5	6
β-strand	169-171	3	6
β-strand	172-178	7	7
β-strand	187	1	8
β-strand	188-195	8	6
β-strand	198-204	7	6
β-strand	209	1	8
β-strand	216-220	5	7
β-strand	221-222	2	6
β-strand	225-226	2	2
α-helix	231-232	2
β-strand	233-238	6	7
α-helix	245	1
β-strand	246	1	9
β-strand	250	1	9
β-strand	251-258	8	7
α-helix	264-266	3
β-strand	271-277	7	6
β-strand	290	1	5
β-strand	292-296	5	6
α-helix	299-301	3
α-helix	306-307	2
β-strand	309-314	6	10
β-strand	319-324	6	11
α-helix	325-327	3
β-strand	338-343	6	10
β-strand	355-358	4	10
β-strand	370-374	5	11
β-strand	380-385	6	11
β-strand	392-399	8	10
β-strand	406-413	8	10

Chain B: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
β-strand	10-12	3	13
β-strand	19-25	7	12
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	59-60	2	13
α-helix	62-64	3
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-97	6	13
β-strand	118-122	5	13

Chain C: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	14
β-strand	9-12	4	15
β-strand	17-23	7	14
β-strand	35-39	5	15
β-strand	45-49	5	15
β-strand	50	1	16
β-strand	54	1	16
β-strand	63-68	6	14
β-strand	71-77	7	14
β-strand	86-92	7	15
β-strand	99-101	3	15
β-strand	105-109	5	15

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	58-60	3	18
β-strand	68-73	6	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-98	7	18
β-strand	114	1	18
β-strand	118-122	5	18

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	19
β-strand	10-13	4	20
β-strand	19-22	4	21
β-strand	24-25	2	19
α-helix	30-32	3
β-strand	34-39	6	20
β-strand	46-50	5	20
β-strand	54-55	2	20
α-helix	56	1
β-strand	63-68	6	21
β-strand	71-76	6	21
α-helix	81-83	3
β-strand	86-91	6	20
β-strand	98-99	2	20
β-strand	103-107	5	20

Chain F: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	11-12	2	23
β-strand	17-25	9	22
α-helix	29-31	3
β-strand	34-40	7	24
β-strand	47-52	6	24
β-strand	58-60	3	24
β-strand	68-70	3	22
β-strand	73	1	22
β-strand	78-84	7	22
α-helix	88-90	3
β-strand	92-99	8	24
β-strand	111	1	24
β-strand	115-117	3	24
β-strand	118-119	2	23

Chain G: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	25
β-strand	5	1	26
β-strand	9-12	4	27
β-strand	18-23	6	26
α-helix	26-30	5
β-strand	35-39	5	27
β-strand	46-49	4	27
β-strand	50	1	28
β-strand	54	1	28
β-strand	63-68	6	26
β-strand	71-76	6	26
α-helix	81-83	3
β-strand	85-90	6	27
β-strand	91-93	3	29
β-strand	98-100	3	29
β-strand	102	1	25
β-strand	105-109	5	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein GP350	A	protein	478	human gammaherpesvirus 4	P03200 (AlphaFold model)
1H5 heavy chain no-CH2CH3	B	protein	248	Homo sapiens
1H5 light chain	C	protein	235	Homo sapiens
1A12 heavy chain no-CH2CH3	D	protein	248	Homo sapiens
1A12 light chain	E	protein	233	Homo sapiens
2E9 heavy chain no-CH2CH3	F	protein	245	Homo sapiens
2E9 light chain	G	protein	235	Homo sapiens

Sequence of entity 1 (A), FASTA

>9MA7_1 Envelope glycoprotein GP350 (chains A)
MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQ
LDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEE
QQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLD
VTLPLSLPTSAQDSNFSVKTQMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVP
SGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQ
SNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTET
DFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVI
FSKAPESTTTSPTLNTTGFADPNTTTGLPSSTHVPTNLTAPASTGPTVSTGSHHHHHH

Sequence of entity 2 (B), FASTA

>9MA7_2 1H5 heavy chain no-CH2CH3 (chains B)
MGWSCIILFLVATATGVHSQVQLVQSGAEVRKPGSSVKVSCEFSGGPFKNSAFSWVRQAP
GQGPEWMGGIIPPFVRGKYAQGFQGRVTITADEHLSTTYMELTGLRSDDTAVYYCARGPS
SGNYNYYYGMDVWGQGTPVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKR
VEPKSCDK

Sequence of entity 3 (C), FASTA

>9MA7_3 1H5 light chain (chains C)
MGWSCIILFLVATATGSWAQSVLTQPPSASGTPGQRVTISCSGSSSNIGSNYVYWYQQLP
GTAPKLLIYRNNQRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCAAWDDSLSGWVF
GGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKA
GVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (D), FASTA

>9MA7_4 1A12 heavy chain no-CH2CH3 (chains D)
MGWSCIILFLVATATGVHSQVQLVQSGAEVKKPGASMKVSCKASGYTFAGYYIHWVRQAP
GQGLEWMGSINPNSGKATYAQRFHGRVTLTREMSINTAYMELTRLTSDDTAIYYCARDAT
YSTSFSPRWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKR
VEPKSCDK

Sequence of entity 5 (E), FASTA

>9MA7_5 1A12 light chain (chains E)
MGWSCIILFLVATATGSWAEIVLTQSPGTLSLSPGERATLSCRASQSISSNSLAWYQQRP
GQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRTFGP
GTKVDIKGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGV
ETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 6 (F), FASTA

>9MA7_6 2E9 heavy chain no-CH2CH3 (chains F)
MGWSCIILFLVATATGVHSQVQLQESGPGLVKPSETLSLICTVSGYSISSGYNWGWIRQP
PGKGLEWIGSINHSGSTYYNPSLKSRVTTSVDTSTNQFSLKLSSVTAADTAVYYCARDSI
MIGYRGLDYWGQGTLVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS
WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP
KSCDK

Sequence of entity 7 (G), FASTA

>9MA7_7 2E9 light chain (chains G)
MGWSCIILFLVATATGSWAQSVVTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLP
GTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAYVF
GTGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKA
GVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9. 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…
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

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