7YP1: EBV gHgL-gp42

Cryo-EM structure of EBV gHgL-gp42 in complex with mAb 10E4 (localized refinement). Determined by electron microscopy at 3.54 Å resolution. Released 31 Jan 2024.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Human gammaherpesvirus 4, Oryctolagus cuniculus
Chains: 4
Atoms: 3,770
Mol. weight: 55.59 kDa
Released: 31 Jan 2024

Explore 7YP1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YP1 contains 13 α-helices and 50 β-strands across 4 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: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	1
β-strand	24-29	6	2
β-strand	32-34	3	2
β-strand	38	1	1
α-helix	43-46	4
α-helix	52-59	8
α-helix	68-72	5
β-strand	75	1	3
β-strand	82	1	4
α-helix	124-130	7
β-strand	135-138	4	5
β-strand	148	1	6
α-helix	149-150	2
β-strand	151-153	3	5
β-strand	156-158	3	7
β-strand	171-173	3	7
β-strand	177-183	7	4
β-strand	193-200	8	4
α-helix	205-206	2
β-strand	207	1	6
α-helix	213-215	3
β-strand	217-221	5	4
β-strand	224-229	6	4
β-strand	231	1	3

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	47-51	5	2
β-strand	61-62	2	8
β-strand	64-65	2	2
β-strand	77	1	2
β-strand	80-81	2	8
α-helix	82-93	12
α-helix	104-116	13
β-strand	118	1	9
α-helix	120-122	3

Chain D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	12	1	11
β-strand	18-24	7	10
β-strand	31	1	9
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	75-80	6	10
α-helix	85-87	3
β-strand	90-95	6	12
β-strand	105-106	2	12
β-strand	110	1	12
β-strand	114	1	11

Chain G: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	18	1	15
β-strand	21-25	5	13
β-strand	34-38	5	14
β-strand	45-49	5	14
β-strand	53-54	2	14
β-strand	56	1	16
β-strand	58	1	16
β-strand	64-65	2	13
β-strand	70-73	4	13
β-strand	76	1	15
α-helix	80-82	3
β-strand	85-89	5	14
β-strand	107-110	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
EBV gH	A	protein	201	Human gammaherpesvirus 4	P03231 (AlphaFold model)
EBV gL	B	protein	80	Human gammaherpesvirus 4	P03212 (AlphaFold model)
10E4 heavy chain	D	protein	115	Oryctolagus cuniculus
10E4 light chain	G	protein	113	Oryctolagus cuniculus

Sequence of entity 1 (A), FASTA

>7YP1_1 EBV gH (chains A)
LSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTS
GTLGIALASAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMT
SKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVH
YANFHNYFVPNLKDMFSRAVT

Sequence of entity 2 (B), FASTA

>7YP1_2 EBV gL (chains B)
LALENISDIYLVSNQTCDGFSLASLNSVISRCANGLNVVSFFISILKRSSSALTGHLREL
LTTLETLYGSFSVEDLFGAN

Sequence of entity 3 (D), FASTA

>7YP1_3 10E4 heavy chain (chains D)
QQVKESGGRLVTPGTPLTLTCTASGFSLSTYWMSWVRQAPGKGLEYIGVIGGSGSTYYAS
WAKGRFTISKTSTTVDLKITSPTTEDTATYFCARDSGAGVRFRFWGPGTLVTVSS

Sequence of entity 4 (G), FASTA

>7YP1_4 10E4 light chain (chains G)
DLVMTQTPASVEAGVGGTVTINCQASENIGSRLAWYQQKPGQPPKLLIYRASTLESGVPS
RFKGSGSGTEFTLTISDLECADAATYYCQCTYGVSITINYGNDFGGGTEVVVK

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 P03231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CZE 3.0 Å, Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand…
7S1B 3.03 Å, Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with…
5T1D 3.1 Å, Crystal structure of EBV gHgL/gp42/E1D1 complex
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
7YP2 3.52 Å, Cryo-EM structure of EBV gHgL-gp42 in complex with mAb 6H2 (localized refinement)
3PHF 3.58 Å, Crystal Structure of the Epstein-Barr virus gH and gL complex
6C5V 4.8 Å, An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of…

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