8TNT: Epstein-Barr virus gH/gL/gp42

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2. Determined by X-ray diffraction at 3.15 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Epstein-Barr virus, Homo sapiens, Mus musculus
Chains: 7
Atoms: 13,731
Mol. weight: 203.23 kDa
Ligands: NAG
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8TNT contains 62 α-helices and 126 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: 32 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	22-29	8	1
β-strand	32-39	8	1
α-helix	40-46	7
α-helix	52-59	8
α-helix	65-73	9
α-helix	77-79	3
β-strand	100-102	3	2
β-strand	119-122	4	2
α-helix	123-130	8
β-strand	134-136	3	3
α-helix	142-145	4
β-strand	148	1	4
β-strand	152-154	3	3
β-strand	156-162	7	5
β-strand	167-173	7	5
β-strand	177-185	9	5
β-strand	191-200	10	5
α-helix	201-203	3
α-helix	205-206	2
β-strand	207	1	4
β-strand	217-220	4	5
β-strand	224-229	6	5
α-helix	232-241	10
α-helix	246-255	10
α-helix	258-274	17
α-helix	285-307	23
β-strand	312-314	3	2
α-helix	315-335	21
β-strand	339-341	3	5
α-helix	346-356	11
α-helix	361-366	6
α-helix	369-382	14
α-helix	391-405	15
α-helix	412-414	3
α-helix	415-432	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	471-474	4
α-helix	477-480	4
β-strand	483	1	6
α-helix	488-494	7
α-helix	503-516	14
α-helix	530-533	4
α-helix	538-540	3
β-strand	541-546	6	6
β-strand	551-555	5	6
β-strand	566-567	2	6
α-helix	575-576	2
β-strand	578-582	5	6
α-helix	583-585	3
α-helix	596	1
β-strand	597-598	2	6
α-helix	599-600	2
β-strand	601-602	2	7
β-strand	617-623	7	7
β-strand	628-634	7	7
α-helix	637-643	7
β-strand	656-661	6	7
β-strand	667-670	4	7

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	47-50	4	1
β-strand	61-65	5	1
α-helix	74-76	3
β-strand	77-81	5	1
α-helix	82-94	13
α-helix	97-99	3
α-helix	102-115	14

Chain C: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	44-46	3
α-helix	48-50	3
α-helix	52-54	3
α-helix	56-61	6
α-helix	67-70	4
β-strand	75	1	3
β-strand	109-111	3	8
β-strand	114-118	5	8
β-strand	123	1	9
α-helix	128-133	6
β-strand	140-141	2	8
α-helix	149-154	6
β-strand	162-163	2	10
β-strand	167	1	11
β-strand	174	1	12
β-strand	175	1	11
β-strand	182	1	12
β-strand	185	1	10
β-strand	193-195	3	10
β-strand	203-204	2	10
β-strand	212	1	9
β-strand	214	1	10
β-strand	215-218	4	8

Chain D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5	1	13
β-strand	9-12	4	14
β-strand	17-20	4	15
β-strand	23	1	13
α-helix	26-28	3
β-strand	35-39	5	14
β-strand	47-50	4	14
β-strand	51	1	16
β-strand	55	1	16
β-strand	64-67	4	15
β-strand	74-78	5	15
β-strand	86-94	9	14
β-strand	98-101	4	14
β-strand	105-109	5	14
β-strand	120-122	3	17
α-helix	123-124	2
α-helix	126-129	4
β-strand	134-135	2	18
β-strand	137-139	3	17
β-strand	150-153	4	19
β-strand	184-185	2	18
β-strand	195-200	6	19
β-strand	205-210	6	19

Chain E: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	20
β-strand	11-12	2	21
β-strand	17-22	6	22
β-strand	23-24	2	20
β-strand	34-39	6	23
β-strand	45-51	7	23
α-helix	53-55	3
β-strand	59-60	2	23
β-strand	68-71	4	22
β-strand	79-84	6	22
α-helix	88-90	3
β-strand	92-98	7	23
β-strand	99	1	24
β-strand	107	1	24
β-strand	114-116	3	23
β-strand	117-118	2	21
α-helix	125-126	2
β-strand	127-131	5	25
α-helix	132-134	3
β-strand	146-152	7	25
β-strand	158-161	4	26
α-helix	174-175	2
β-strand	176-177	2	25
β-strand	183-187	5	25
β-strand	202-207	6	26
α-helix	208-210	3
β-strand	212-217	6	26

Chain F: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	27
β-strand	10-14	5	28
β-strand	19-25	7	27
β-strand	30-31	2	29
β-strand	34-35	2	29
β-strand	37-42	6	28
β-strand	48-53	6	28
β-strand	57-58	2	28
α-helix	59	1
β-strand	66-71	6	27
β-strand	74-79	6	27
β-strand	89-94	6	28
β-strand	107-111	5	28
α-helix	116-117	2
β-strand	118-122	5	30
α-helix	126-129	4
β-strand	133-143	11	30
β-strand	148-154	7	31
β-strand	163-167	5	30
α-helix	168-171	4
β-strand	177-186	10	30
β-strand	196-202	7	31
β-strand	209-213	5	31

Chain G: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	32
β-strand	11	1	33
β-strand	19-25	7	32
β-strand	33-40	8	34
β-strand	44-51	8	34
β-strand	59-60	2	34
β-strand	69-73	5	32
β-strand	78-82	5	32
α-helix	88-90	3
β-strand	92-99	8	34
α-helix	101-103	3
β-strand	105-107	3	34
β-strand	112-114	3	34
β-strand	115	1	33
α-helix	120-121	2
β-strand	127-129	3	35
β-strand	143-150	8	35
β-strand	156-158	3	36
β-strand	169-170	2	35
α-helix	171-173	3
β-strand	174-175	2	35
β-strand	181-187	7	35
β-strand	202-205	4	36
β-strand	210-212	3	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A	protein	656	Epstein-Barr virus	P03231 (AlphaFold model)
Envelope glycoprotein L	B	protein	112	Epstein-Barr virus	P03212 (AlphaFold model)
Glycoprotein 42	C	protein	191	Epstein-Barr virus	P03205 (AlphaFold model)
769C2 light chain	D	protein	216	Homo sapiens
769C2 heavy chain	E	protein	232	Homo sapiens
F-2-1 light chain	F	protein	218	Mus musculus
F-2-1 heavy chain	G	protein	230	Mus musculus

Sequence of entity 1 (A), FASTA

>8TNT_1 Envelope glycoprotein H (chains A)
SLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKT
SGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTML
PNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVF
GKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTA
ASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWL
AKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRL
ATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTT
QGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQE
ATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDR
EVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFA
LLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Sequence of entity 2 (B), FASTA

>8TNT_2 Envelope glycoprotein L (chains B)
WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGL
NVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHR

Sequence of entity 3 (C), FASTA

>8TNT_3 Glycoprotein 42 (chains C)
GGGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHWTPTLHTFQVPQ
NYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVV
TRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLK
PCLCVSQRSNS

Sequence of entity 4 (D), FASTA

>8TNT_4 769C2 light chain (chains D)
QSVLTQPASVSGSLGQSVTISCTGTSSDVGGYDYVSWYQQHPGKALKLMIFEVNNRPSGV
STRFSGSKSGNTASLTISGLQAEDEADYYCNSYSTTTTWVFGGGTSLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (E), FASTA

>8TNT_5 769C2 heavy chain (chains E)
EVQLVESGGGLVKPGGSLRLSCAASGFTFSTYAMDWVRQAPGKGLEWVSLISSRSSNIYY
SDSVKGRFTISRDNAKNSLFLQMNSLRAEDTAVYYCAREAGGFHSHFDMWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 6 (F), FASTA

>8TNT_6 F-2-1 light chain (chains F)
DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPKLLIYLASNLES
GVPARFSGSGSGTDFTLNIHPVEEEDAATYYCLHSRDLPPTFGGGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 7 (G), FASTA

>8TNT_7 F-2-1 heavy chain (chains G)
EVKLLESGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINY
TSSLKDKFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGDWWYFDVWGAGTTVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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 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
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)
7YP1 3.54 Å, Cryo-EM structure of EBV gHgL-gp42 in complex with mAb 10E4 (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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