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

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10. Determined by X-ray diffraction at 3.36 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 3.36 Å
Organisms: Human herpesvirus 4 strain B95-8, Macaca fascicularis
Chains: 10
Atoms: 20,293
Mol. weight: 312.86 kDa
Ligands: NAG
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8TNN contains 103 α-helices and 184 β-strands across 10 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: 30 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	23-27	5	1
β-strand	34-38	5	1
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-74	10
β-strand	75	1	2
β-strand	81-83	3	3
α-helix	94-96	3
β-strand	100-102	3	4
β-strand	119-122	4	4
α-helix	123-130	8
β-strand	134-138	5	5
α-helix	144-147	4
β-strand	148	1	6
α-helix	149-150	2
β-strand	151-154	4	5
β-strand	156-162	7	3
β-strand	167-173	7	3
β-strand	177-185	9	3
β-strand	191-200	10	3
α-helix	205-206	2
β-strand	207	1	6
α-helix	213-215	3
β-strand	217-220	4	3
β-strand	224-230	7	3
β-strand	231	1	2
α-helix	232-239	8
α-helix	246-255	10
α-helix	258-275	18
α-helix	285-307	23
β-strand	312-314	3	4
α-helix	315-335	21
β-strand	339-341	3	3
α-helix	346-357	12
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-406	15
α-helix	412-414	3
α-helix	415-433	19
α-helix	440-453	14
α-helix	456-468	13
α-helix	471-473	3
α-helix	477-480	4
β-strand	483	1	7
α-helix	488-493	6
α-helix	503-516	14
α-helix	532-534	3
β-strand	535	1	8
β-strand	541-546	6	7
β-strand	550-555	6	7
β-strand	560	1	8
β-strand	566-567	2	7
β-strand	578-583	6	7
α-helix	596	1
β-strand	597-598	2	7
α-helix	599	1
β-strand	601-602	2	9
β-strand	618-623	6	9
β-strand	627-633	7	9
α-helix	637-644	8
β-strand	656-661	6	9
β-strand	667-670	4	9

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	47-50	4	1
β-strand	62-65	4	1
β-strand	77-80	4	1
α-helix	82-94	13
α-helix	103-116	14
α-helix	121-123	3

Chain C: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	45-50	6
α-helix	52-54	3
α-helix	56-60	5
β-strand	75-76	2	5
β-strand	109-111	3	10
β-strand	112	1	11
β-strand	114-118	5	10
β-strand	123	1	12
α-helix	128-135	8
β-strand	139-141	3	10
α-helix	145-147	3
α-helix	150-154	5
β-strand	162-164	3	13
β-strand	166-167	2	14
β-strand	175-176	2	14
β-strand	185	1	13
β-strand	193-195	3	13
β-strand	203-204	2	13
β-strand	212	1	12
β-strand	214	1	13
β-strand	215-219	5	10

Chain D: 31 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	15
β-strand	33-39	7	15
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-74	10
β-strand	75	1	16
β-strand	81-83	3	3
α-helix	94-96	3
β-strand	100-102	3	17
α-helix	112-113	2
β-strand	119-122	4	17
α-helix	123-130	8
β-strand	134-138	5	18
α-helix	144-147	4
β-strand	148	1	19
β-strand	151-154	4	18
β-strand	156-162	7	3
β-strand	167-173	7	3
β-strand	177-185	9	3
β-strand	191-200	10	3
α-helix	205-206	2
β-strand	207	1	19
α-helix	213-216	4
β-strand	217-220	4	3
β-strand	224-230	7	3
β-strand	231	1	16
α-helix	232-241	10
α-helix	246-255	10
α-helix	258-273	16
α-helix	274-276	3
α-helix	285-308	24
β-strand	312-313	2	17
α-helix	317-320	4
α-helix	322-336	15
β-strand	339-341	3	3
α-helix	346-357	12
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-406	15
α-helix	412-414	3
α-helix	415-433	19
α-helix	440-453	14
α-helix	456-468	13
α-helix	471-473	3
α-helix	477-480	4
β-strand	483	1	20
α-helix	488-493	6
α-helix	503-516	14
β-strand	541-547	7	20
β-strand	550-555	6	20
β-strand	566-567	2	20
β-strand	578-580	3	20
β-strand	583	1	20
α-helix	596	1
β-strand	597-598	2	20
α-helix	599	1
β-strand	601-602	2	21
β-strand	618-623	6	21
β-strand	628-633	6	21
α-helix	637-645	9
β-strand	656-661	6	21
β-strand	667-670	4	21

Chain E: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	47-50	4	15
β-strand	61-64	4	15
β-strand	78-81	4	15
α-helix	82-94	13
α-helix	103-116	14
α-helix	121-123	3

Chain F: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	45-50	6
α-helix	52-54	3
α-helix	56-60	5
β-strand	75-76	2	18
β-strand	109-111	3	22
β-strand	112	1	23
β-strand	114-118	5	22
β-strand	123	1	24
α-helix	128-133	6
β-strand	140-141	2	22
α-helix	149-154	6
β-strand	162-164	3	25
β-strand	166-167	2	26
β-strand	175-176	2	26
β-strand	185	1	25
β-strand	193-195	3	25
β-strand	203-204	2	25
β-strand	212	1	24
β-strand	214	1	25
β-strand	215-219	5	22

Chain G: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	27
β-strand	8-12	5	28
α-helix	16	1
β-strand	17-22	6	27
α-helix	26-28	3
β-strand	29	1	11
β-strand	32-36	5	28
β-strand	43-46	4	28
β-strand	47	1	29
β-strand	51	1	29
β-strand	60-65	6	27
β-strand	68-73	6	27
β-strand	83-89	7	28
β-strand	94-96	3	28
α-helix	97	1
β-strand	100-105	6	28
α-helix	110-112	3
β-strand	113-117	5	30
α-helix	121-125	5
β-strand	129-138	10	30
β-strand	143-148	6	31
β-strand	153	1	31
β-strand	158-160	3	30
β-strand	164-165	2	30
β-strand	171-179	9	30
α-helix	181-183	3
β-strand	191-196	6	31
β-strand	199-203	5	31

Chain H: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	32
β-strand	11-12	2	33
β-strand	15-25	11	32
β-strand	35-42	8	34
β-strand	46-55	10	34
β-strand	59-63	5	34
α-helix	65-67	3
β-strand	71-72	2	32
β-strand	75-76	2	32
β-strand	81-89	9	32
α-helix	91-93	3
β-strand	95-102	8	34
β-strand	110	1	34
β-strand	114-116	3	34
β-strand	117-118	2	33
α-helix	121-123	3
α-helix	125-126	2
β-strand	127-129	3	35
β-strand	143-152	10	35
β-strand	158-161	4	36
β-strand	170-172	3	35
α-helix	173-175	3
β-strand	176-177	2	35
β-strand	183-191	9	35
α-helix	193-195	3
β-strand	201-207	7	36
α-helix	208-210	3
β-strand	212-218	7	36

2 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
Envelope glycoprotein H	A, D	protein	658	Human herpesvirus 4 strain B95-8	P03231 (AlphaFold model)
Envelope glycoprotein L	B, E	protein	112	Human herpesvirus 4 strain B95-8	P03212 (AlphaFold model)
Glycoprotein 42	C, F	protein	191	Human herpesvirus 4 strain B95-8	P03205 (AlphaFold model)
A10 light chain	G, I	protein	213	Macaca fascicularis
A10 heavy chain	H, J	protein	234	Macaca fascicularis

Sequence of entity 1 (A, D), FASTA

>8TNN_1 Envelope glycoprotein H (chains A, D)
AASLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIY
KTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGT
MLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSL
VFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTM
TAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLR
WLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYAL
RLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNV
TTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAP
QEATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISS
DREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCG
FALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Sequence of entity 2 (B, E), FASTA

>8TNN_2 Envelope glycoprotein L (chains B, E)
WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGL
NVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHR

Sequence of entity 3 (C, F), FASTA

>8TNN_3 Glycoprotein 42 (chains C, F)
GGGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHWTPTLHTFQVPQ
NYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVV
TRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLK
PCLCVSQRSNS

Sequence of entity 4 (G, I), FASTA

>8TNN_4 A10 light chain (chains G, I)
NSYELTQPPSVSAASGQTARITCGGDNIGSKNVQWYQQKPAQAPVLVIYADSKRPSGVPE
RFSGSNSGNTATLTISGVEAGDEADYYCQVWDRSSNIFGVGTRLTVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (H, J), FASTA

>8TNN_5 A10 heavy chain (chains H, J)
NSQVQLQESGPGLVKPSQTLSLTCAISGDSVSSNSATWNWIRQSPSRGLEWLGRTYYRSK
WYYDYAQSVQNRISINPDTSKNQFSLQLNSVTPEDMAVYYCARGDFDAFDFWGQGLRVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

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
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…
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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