8TOO: Epstein-Barr virus gp42

Crystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Mus musculus, Epstein-Barr virus
Chains: 12
Atoms: 17,213
Mol. weight: 258.82 kDa
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8TOO contains 68 α-helices and 224 β-strands across 12 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.

Chains A and C: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	44-49	6	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-150	7	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-198	8	5
β-strand	205-210	6	5

Chain B: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	6
α-helix	7	1
β-strand	10-12	3	7
β-strand	18-23	6	6
α-helix	29-31	3
β-strand	33-40	8	7
β-strand	45-52	8	7
β-strand	58-60	3	7
β-strand	68-73	6	6
β-strand	78-83	6	6
β-strand	92-100	9	7
β-strand	103-110	8	7
β-strand	114-118	5	7
α-helix	122-123	2
β-strand	124	1	8
β-strand	127-131	5	9
β-strand	139	1	9
β-strand	142-152	11	9
β-strand	153	1	8
β-strand	158-161	4	10
β-strand	171-172	2	9
α-helix	173-175	3
β-strand	176-177	2	9
β-strand	183-192	10	9
β-strand	202-207	6	10
α-helix	208-210	3
β-strand	212-217	6	10

Chain D: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
α-helix	7	1
β-strand	10-12	3	17
β-strand	18-24	7	16
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	45-52	8	17
β-strand	58-60	3	17
β-strand	68-73	6	16
β-strand	78-83	6	16
β-strand	92-100	9	17
β-strand	103-110	8	17
β-strand	114-118	5	17
α-helix	121-123	3
β-strand	124	1	18
β-strand	127-131	5	19
β-strand	142-152	11	19
β-strand	153	1	18
β-strand	158-161	4	20
α-helix	162-164	3
β-strand	170-172	3	19
α-helix	173-175	3
β-strand	176-177	2	19
β-strand	183-192	10	19
β-strand	201-207	7	20
α-helix	208-210	3
β-strand	212-218	7	20

Chain E: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	21
β-strand	10-14	5	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	44-49	6	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-90	7	22
α-helix	96	1
β-strand	97-98	2	22
β-strand	102-107	6	22
β-strand	111	1	23
α-helix	112-113	2
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	145-150	6	25
β-strand	153-154	2	25
α-helix	155	1
β-strand	159-163	5	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-188	6
β-strand	191-197	7	25
β-strand	205-210	6	25

Chain F: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	26
β-strand	10-14	5	27
β-strand	19-25	7	26
β-strand	33-38	6	27
β-strand	44-49	6	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-67	6	26
β-strand	70-75	6	26
α-helix	80-82	3
β-strand	85-90	6	27
α-helix	96	1
β-strand	97-98	2	27
β-strand	102-107	6	27
β-strand	111	1	28
α-helix	112-113	2
β-strand	114-118	5	29
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	145-150	6	30
β-strand	153-154	2	30
α-helix	155	1
β-strand	159-163	5	29
α-helix	164-167	4
β-strand	173-182	10	29
α-helix	183-188	6
β-strand	191-197	7	30
β-strand	205-210	6	30

Chain G: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	31
α-helix	7	1
β-strand	10-12	3	32
β-strand	18-25	8	31
α-helix	29-31	3
β-strand	33-39	7	32
β-strand	45-52	8	32
β-strand	58-60	3	32
β-strand	68-73	6	31
β-strand	78-83	6	31
β-strand	92-100	9	32
β-strand	103-110	8	32
β-strand	114-118	5	32
α-helix	122-123	2
β-strand	124	1	33
β-strand	127-131	5	34
β-strand	142-152	11	34
β-strand	153	1	33
β-strand	158-161	4	35
α-helix	162-164	3
β-strand	170-172	3	34
α-helix	173-175	3
β-strand	176-177	2	34
β-strand	183-192	10	34
α-helix	193-195	3
β-strand	196	1	36
β-strand	199	1	36
β-strand	202-207	6	35
α-helix	208-210	3
β-strand	212-217	6	35

Chain H: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	37
α-helix	7	1
β-strand	10-12	3	38
β-strand	18-25	8	37
α-helix	29-31	3
β-strand	33-39	7	38
β-strand	45-52	8	38
β-strand	58-60	3	38
β-strand	68-73	6	37
β-strand	78-83	6	37
β-strand	92-100	9	38
β-strand	103-110	8	38
β-strand	114-118	5	38
α-helix	122-123	2
β-strand	124	1	39
β-strand	127-131	5	40
β-strand	142-152	11	40
β-strand	153	1	39
β-strand	158-161	4	41
α-helix	162-164	3
β-strand	170-172	3	40
α-helix	173-175	3
β-strand	176-177	2	40
β-strand	183-192	10	40
β-strand	202-207	6	41
α-helix	208-210	3
β-strand	212-217	6	41

Chain I: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	109-111	3	42
β-strand	114-118	5	42
β-strand	123	1	43
α-helix	127-133	7
β-strand	140-141	2	42
α-helix	149-154	6
β-strand	162-164	3	44
β-strand	167-168	2	45
β-strand	174-175	2	45
β-strand	182	1	45
β-strand	185	1	44
β-strand	192-195	4	44
β-strand	203-205	3	44
β-strand	212	1	43
β-strand	214	1	44
β-strand	215-219	5	42

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4C12 light chain	A, C, E, F	protein	214	Mus musculus
4C12 heavy chain	B, D, G, H	protein	234	Mus musculus
Glycoprotein 42	I, J, K, L	protein	139	Epstein-Barr virus	P03205 (AlphaFold model)

Sequence of entity 1 (A, C, E, F), FASTA

>8TOO_1 4C12 light chain (chains A, C, E, F)
DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLRSGVPS
RFSGSGSGTDYSLTINNLEQEDIATYFCQQGNTLPFTFGSGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D, G, H), FASTA

>8TOO_2 4C12 heavy chain (chains B, D, G, H)
EVQLQQSGPELVKPGASVKISCKASGYTFTDYNMHWVKQSHGKNLEWIGFIYLYNGGTGY
NQNFKSKATLTVDNSSSTAYMELRSLTSEDSAVFYCARDYYGNPYAMDYWGQGTSVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQGP

Sequence of entity 3 (I, J, K, L), FASTA

>8TOO_3 Glycoprotein 42 (chains I, J, K, L)
LHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGP
TPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVS
HHECSFLKPCLCVSQRSNS

Primary citation

Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells. Bu, W., Kumar, A., Board, N.L. et al. Immunity (2024) 57:559-573.e6. DOI 10.1016/j.immuni.2024.02.008 · PubMed

Other PDB entries of the same protein (UniProt P03205 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FD4 2.4 Å, Crystal Structure of Epstein-Barr virus gp42 protein
1KG0 2.65 Å, Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor…
7S1B 3.03 Å, Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with…
5W0K 3.1 Å, Crystal structure of EBV gHgL/CL40/gp42 N-domain
8TNT 3.15 Å, Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and…
7S07 3.29 Å, Crystal structure of Epstein-Barr virus glycoprotein gH/gL/gp42-peptide in complex with…
8TNN 3.36 Å, Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10
7YOY 3.64 Å, Cryo-EM structure of EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3 (localized refinement)
6C5V 4.8 Å, An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of…

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