7S1B: Envelope glycoprotein H

Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7. Determined by X-ray diffraction at 3.03 Å resolution. Released 9 Nov 2022.

Method: X-ray diffraction
Resolution: 3.03 Å
Organisms: Human gammaherpesvirus 4, Homo sapiens
Chains: 7
Atoms: 12,257
Mol. weight: 184.64 kDa
Ligands: NAG
Released: 9 Nov 2022

Explore 7S1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S1B contains 56 α-helices and 118 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, 35 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	1
β-strand	34-39	6	1
α-helix	40-45	6
α-helix	52-59	8
α-helix	65-74	10
β-strand	75	1	2
β-strand	82-83	2	3
α-helix	93-96	4
α-helix	99	1
β-strand	100-102	3	4
β-strand	103	1	5
β-strand	106	1	5
β-strand	119-122	4	4
α-helix	123-130	8
β-strand	134-138	5	6
α-helix	142-147	6
β-strand	148	1	7
β-strand	151-154	4	6
β-strand	156-162	7	3
β-strand	167-170	4	3
β-strand	173	1	3
β-strand	177-184	8	3
β-strand	192-200	9	3
α-helix	205-206	2
β-strand	207	1	7
α-helix	214-216	3
β-strand	217-220	4	3
β-strand	224-229	6	3
β-strand	231	1	2
α-helix	232-238	7
α-helix	246-255	10
α-helix	258-273	16
α-helix	285-306	22
β-strand	312-314	3	4
α-helix	315-335	21
β-strand	339-341	3	3
α-helix	346-355	10
α-helix	361-366	6
α-helix	369-382	14
α-helix	391-406	16
α-helix	408	1
α-helix	411-414	4
α-helix	415-432	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	471-473	3
α-helix	477-479	3
β-strand	483	1	8
α-helix	488-494	7
α-helix	504-516	13
α-helix	532-534	3
β-strand	535	1	9
α-helix	538-540	3
β-strand	541-546	6	8
β-strand	550-555	6	8
β-strand	560	1	9
β-strand	566-567	2	8
β-strand	578-583	6	8
α-helix	595-596	2
β-strand	597-598	2	8
α-helix	599-600	2
β-strand	601-602	2	10
β-strand	618-623	6	10
β-strand	627-633	7	10
α-helix	637-644	8
β-strand	656-661	6	10
β-strand	667-670	4	10

Chain B: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	32-35	4
α-helix	42-44	3
β-strand	47-50	4	1
β-strand	61-65	5	1
α-helix	71-73	3
β-strand	77-81	5	1
α-helix	82-94	13
α-helix	97-99	3
α-helix	103-117	15

Chain C: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	48-50	3
α-helix	52-54	3
α-helix	56-59	4
α-helix	67-70	4
β-strand	75	1	6

Chain H: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	11
β-strand	11-12	2	12
β-strand	18-25	8	11
β-strand	33-39	7	13
β-strand	46-52	7	13
β-strand	57-59	3	13
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	87-89	3
β-strand	91-98	8	13
β-strand	112-115	4	13
α-helix	116-118	3
β-strand	119-121	3	13
β-strand	122-123	2	12
β-strand	129	1	14
β-strand	132-136	5	15
β-strand	147-157	11	15
β-strand	158	1	14
β-strand	162-166	5	16
α-helix	167-169	3
β-strand	171	1	16
β-strand	175-177	3	15
α-helix	178-180	3
β-strand	181-182	2	15
β-strand	188-197	10	15
β-strand	207-212	6	16
β-strand	217-222	6	16

Chain L: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	35-39	5	18
β-strand	46-50	5	18
β-strand	54-55	2	18
β-strand	63-68	6	17
β-strand	71-76	6	17
α-helix	81-83	3
β-strand	85-91	7	18
β-strand	98-99	2	18
β-strand	100	1	17
β-strand	103-107	5	18
β-strand	115-119	5	19
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	19
β-strand	145-151	7	20
β-strand	154-155	2	20
α-helix	156	1
β-strand	160-164	5	19
α-helix	165-168	4
β-strand	174-183	10	19
α-helix	184-188	5
β-strand	192-199	8	20
β-strand	206-211	6	20

Chain X: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	18-21	4	21
β-strand	34-39	6	22
β-strand	46-51	6	22
β-strand	58-60	3	22
β-strand	70-73	4	21
α-helix	74-76	3
β-strand	78-83	6	21
α-helix	87-89	3
β-strand	93-101	9	22
β-strand	104-110	7	22
β-strand	146	1	23
β-strand	158-160	3	24
β-strand	170-172	3	23
β-strand	187-189	3	23
β-strand	204-206	3	24

Chain Y: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	25
β-strand	5	1	26
β-strand	18-20	3	27
β-strand	23	1	26
β-strand	35-38	4	28
β-strand	64-66	3	27
β-strand	69	1	26
β-strand	72	1	26
β-strand	75-77	3	27
β-strand	87-88	2	29
β-strand	89-92	4	28
β-strand	100	1	28
β-strand	101-102	2	25
β-strand	105-106	2	29
α-helix	112-114	3
β-strand	115	1	30
β-strand	120-121	2	31
β-strand	138-143	6	31
β-strand	144	1	30
β-strand	149-153	5	32
β-strand	170	1	31
β-strand	176-180	5	31
α-helix	186-189	4
β-strand	195-200	6	32
β-strand	205-210	6	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A	protein	657	Human gammaherpesvirus 4	P03231 (AlphaFold model)
Envelope glycoprotein L	B	protein	114	Human gammaherpesvirus 4	P03212 (AlphaFold model)
770F7 Fab heavy chain	H	protein	230	Homo sapiens
770F7 Fab light chain	L	protein	215	Homo sapiens
769C2 Fab heavy chain	X	protein	225	Homo sapiens
769C2 Fab light chain	Y	protein	215	Homo sapiens
Soluble gp42	C	protein	33	Human gammaherpesvirus 4	P03205 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7S1B_1 Envelope glycoprotein H (chains A)
ASLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYK
TSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTM
LPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLV
FGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMT
AASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRW
LAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALR
LATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVT
TQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQ
EATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSD
REVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGF
ALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Sequence of entity 2 (B), FASTA

>7S1B_2 Envelope glycoprotein L (chains B)
WAYPCCHVTQLAAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGL
NVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHRGG

Sequence of entity 3 (H), FASTA

>7S1B_3 770F7 Fab heavy chain (chains H)
QVQFQQWGAGLLKPSETLSLTCGVYGGSLSGYYWSWIRQTPGKGLEWIGEINHTGTTNYN
PSLKSRVTMSVDTSKNQFSLKMSSLTAADTALYYCAREGAPRWALKRPSNWFDPWGQGTL
VTVSSASTKGPSVFPLAPSSASTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 4 (L), FASTA

>7S1B_4 770F7 Fab light chain (chains L)
EIVLTQSPVSLSLSPGERATLSCRASQSLSSTYLAWYQQIPGQAPRLLIYGASSRAAGIP
DRFSGGGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRSFGQGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (X), FASTA

>7S1B_5 769C2 Fab heavy chain (chains X)
EVQLVESGGGLVKPGGSLRLSCAASGFTFSTYAMDWVRQAPGKGLEWVSLISSRSSNIYY
SDSVKGNFTISRDNAKNSLFLQMNSLRAEDTAVYYCAREAGGFHSHFDMWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 6 (Y), FASTA

>7S1B_6 769C2 Fab light chain (chains Y)
QSVLTQPASVSGSLGQSVTISCTGTSSDVGGYDYVSWYQQHPGKNPKLMIFEVNNRPSGV
STRFSGSKSGNTASLTISGLQAEDEADYYCNSYSTTTTWVFGGGTSLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Sequence of entity 7 (C), FASTA

>7S1B_7 Soluble gp42 (chains C)
KPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Epstein-Barr virus gH/gL has multiple sites of vulnerability for virus neutralization and fusion inhibition. Chen, W.H., Kim, J., Bu, W. et al. Immunity (2022) 55:2135-2148.e6. DOI 10.1016/j.immuni.2022.10.003 · 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…
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)
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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