7YOY: EBV gHgL-gp42

Cryo-EM structure of EBV gHgL-gp42 in complex with mAbs 3E8 and 5E3 (localized refinement). Determined by electron microscopy at 3.64 Å resolution. Released 31 Jan 2024.

Method: Electron microscopy
Resolution: 3.64 Å
Organisms: Human gammaherpesvirus 4, Oryctolagus cuniculus
Chains: 5
Atoms: 4,517
Mol. weight: 64.25 kDa
Released: 31 Jan 2024

Explore 7YOY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YOY contains 3 α-helices and 61 β-strands across 5 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 C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	110-111	2	1
β-strand	114-118	5	1
β-strand	123	1	2
α-helix	128-133	6
β-strand	140-141	2	1
α-helix	149-154	6
β-strand	162-163	2	3
β-strand	167	1	4
β-strand	175	1	4
β-strand	185	1	3
β-strand	193-195	3	3
β-strand	203-204	2	3
β-strand	212	1	2
β-strand	215-219	5	1

Chain E: 0 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
β-strand	10	1	6
β-strand	17-23	7	5
β-strand	33-38	6	7
β-strand	44-50	7	7
β-strand	56-58	3	7
β-strand	66-70	5	5
β-strand	74-79	6	5
β-strand	88-94	7	7
β-strand	95-96	2	8
β-strand	99-100	2	9
β-strand	103-104	2	9
β-strand	107-108	2	8
β-strand	115-117	3	7
β-strand	118	1	6

Chain F: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	10
β-strand	12	1	11
β-strand	18-22	5	10
β-strand	34-39	6	12
β-strand	46-51	6	12
β-strand	57-59	3	12
β-strand	67-71	5	10
β-strand	76-80	5	10
β-strand	89-95	7	12
β-strand	104	1	12
β-strand	108-110	3	12
β-strand	112	1	11

Chain I: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
β-strand	20-25	6	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
β-strand	63-67	5	13
β-strand	70-74	5	13
β-strand	85-90	6	14
β-strand	91-93	3	15
β-strand	98-100	3	15

Chain J: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	16
β-strand	10-11	2	17
β-strand	19-24	6	16
β-strand	33-37	5	18
α-helix	43-44	2
β-strand	45-49	5	18
β-strand	54	1	18
β-strand	62-67	6	16
β-strand	70-75	6	16
β-strand	85-86	2	17
β-strand	87-92	6	18
β-strand	99-101	3	18
β-strand	106-108	3	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble gp42	C	protein	136	Human gammaherpesvirus 4	P03205 (AlphaFold model)
5E3 heavy chain	E	protein	121	Oryctolagus cuniculus
3E8 heavy chain	F	protein	113	Oryctolagus cuniculus
5E3 light chain	I	protein	111	Oryctolagus cuniculus
3E8 light chain	J	protein	112	Oryctolagus cuniculus

Sequence of entity 1 (C), FASTA

>7YOY_1 Soluble gp42 (chains C)
FQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPD
ILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHE
CSFLKPCLCVSQRSNS

Sequence of entity 2 (E), FASTA

>7YOY_2 5E3 heavy chain (chains E)
QPVEESGGRLVTPGTPLTLTCTVSGFSLSTYAMSWVRQAPGKGLEWIGTISASDTTYFAN
WTKGRFTISKASTTVDLKITSPTTEDTATFFCARFSAYESNRDYFDTFDPWGPGTLVTVS
S

Sequence of entity 3 (F), FASTA

>7YOY_3 3E8 heavy chain (chains F)
QPVKESGGRLVTPGTPLTLTCTASGFSLSSYWMSWVRQARGKGLEWIGTATAGGSAWYAS
WAKGRFTISRTSTTVELRMTSLTTEDTATYFCARDPPGHSGLWGRGTLVTVSS

Sequence of entity 4 (I), FASTA

>7YOY_4 5E3 light chain (chains I)
DVVMTQTPSPVSAAVGGTVTIKCQASQNIYRDLAWYQQNPGQPPKLLIYGASNLASGVPS
RFSGSGSGTEYILTISDLECADAATYYCQCSAYGSGYAAHAFGGGTKVDIK

Sequence of entity 5 (J), FASTA

>7YOY_5 3E8 light chain (chains J)
DLVMTQTPASVEAAVGGTVTIKCQASESIGNALAWYQQKPGQPPKLLIYDTSNLASGVSS
RFRGSGSGTQFTLTISDLECADAATYYCQTYYYSGVTTTYQAFGGGTEVDVK

Primary citation

Non-overlapping epitopes on the gHgL-gp42 complex for the rational design of a triple-antibody cocktail against EBV infection. Hong, J., Zhong, L., Liu, L. et al. Cell Rep Med (2023) 4:101296-101296. DOI 10.1016/j.xcrm.2023.101296 · 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
8TOO 2.6 Å, Crystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12
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
6C5V 4.8 Å, An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of…

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