7S07: Envelope glycoprotein H

Crystal structure of Epstein-Barr virus glycoprotein gH/gL/gp42-peptide in complex with human neutralizing antibodies 769B10 and 769C2. Determined by X-ray diffraction at 3.29 Å resolution. Released 9 Nov 2022.

Method: X-ray diffraction
Resolution: 3.29 Å
Organisms: Human gammaherpesvirus 4, Homo sapiens
Chains: 7
Atoms: 12,693
Mol. weight: 183.37 kDa
Ligands: NAG
Released: 9 Nov 2022

Explore 7S07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S07 contains 48 α-helices and 133 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: 30 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	23-28	6	1
β-strand	35-38	4	1
α-helix	40-46	7
α-helix	52-56	5
α-helix	65-72	8
β-strand	75	1	2
β-strand	82-83	2	3
α-helix	87-89	3
α-helix	93-96	4
β-strand	100-102	3	4
β-strand	119-122	4	4
α-helix	123-130	8
β-strand	134-136	3	5
β-strand	148	1	6
α-helix	149-150	2
β-strand	152-154	3	5
β-strand	156-161	6	3
β-strand	167-173	7	3
β-strand	177-186	10	3
β-strand	190-200	11	3
α-helix	201-203	3
α-helix	204-206	3
β-strand	207	1	6
β-strand	217-220	4	3
β-strand	224-229	6	3
β-strand	231	1	2
α-helix	232-241	10
α-helix	246-255	10
α-helix	258-274	17
α-helix	285-306	22
β-strand	312-314	3	4
α-helix	315-335	21
β-strand	339-341	3	3
α-helix	346-354	9
α-helix	364-366	3
α-helix	369-382	14
α-helix	392-405	14
α-helix	408	1
α-helix	411-414	4
α-helix	415-432	18
α-helix	440-453	14
α-helix	458-465	8
α-helix	472-474	3
β-strand	483	1	7
α-helix	488-491	4
α-helix	492-494	3
α-helix	503-513	11
β-strand	535	1	8
β-strand	541-546	6	7
β-strand	550-555	6	7
β-strand	560	1	8
β-strand	566-568	3	7
β-strand	577-583	7	7
α-helix	595-596	2
β-strand	597-598	2	7
α-helix	599-600	2
β-strand	601-602	2	9
β-strand	618-623	6	9
β-strand	628	1	9
β-strand	632-633	2	9
α-helix	637-644	8
β-strand	656-661	6	9
β-strand	667-670	4	9

Chain B: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	46-51	6	1
β-strand	61-65	5	1
β-strand	78-81	4	1
α-helix	82-94	13
α-helix	102-116	15

Chain C: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	48-50	3
α-helix	52-54	3
α-helix	56-59	4
β-strand	75	1	5

Chain H: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	27
β-strand	6-7	2	28
β-strand	10-12	3	29
β-strand	17-22	6	28
β-strand	25	1	27
α-helix	29-31	3
β-strand	33-39	7	30
β-strand	45-51	7	30
β-strand	57-59	3	30
β-strand	68-72	5	28
β-strand	77-83A	7	28
α-helix	84-86	3
β-strand	88-90	3	29
β-strand	91-97	7	30
α-helix	100-100B	3
β-strand	100H-100M	6	30
β-strand	104-108	5	29
β-strand	117-121	5	31
β-strand	132	1	32
β-strand	136-140	5	31
β-strand	142	1	33
β-strand	148-151	4	34
β-strand	160-162	3	31
α-helix	163-165	3
β-strand	167	1	33
β-strand	173	1	33
β-strand	176-179	4	31
β-strand	182	1	32
β-strand	186	1	35
β-strand	189	1	35
β-strand	192-197	6	34
β-strand	202-207	6	34

Chain L: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	10-12	3	37
β-strand	19-25	7	36
β-strand	33-38	6	37
β-strand	44-49	6	37
β-strand	53-54	2	37
β-strand	62-63	2	36
β-strand	70-75	6	36
α-helix	80-82	3
β-strand	85-90	6	37
α-helix	96	1
β-strand	97-98	2	37
β-strand	102-105	4	37
β-strand	111	1	38
β-strand	116-118	3	39
α-helix	119-121	3
α-helix	122-125	4
β-strand	131-139	9	39
β-strand	140	1	38
β-strand	145-148	4	40
β-strand	159-160	2	39
β-strand	163	1	39
β-strand	173-180	8	39
α-helix	183-186	4
β-strand	194-197	4	40
β-strand	205	1	40

Chain X: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	10
β-strand	12	1	11
β-strand	16-21	6	12
β-strand	22-24	3	10
β-strand	34	1	13
β-strand	37-39	3	14
β-strand	46-47	2	14
β-strand	50-51	2	15
α-helix	52A-54	3
β-strand	57-58	2	15
β-strand	67-70	4	12
β-strand	79-82B	6	12
β-strand	88-91	4	14
β-strand	94-95	2	13
β-strand	100C-100E	3	13
β-strand	105-106	2	14
β-strand	108	1	11
β-strand	114	1	16
β-strand	117-120	4	17
β-strand	137-142	6	17
β-strand	143	1	16
β-strand	149-151	3	18
β-strand	161-163	3	17
α-helix	164-165	2
β-strand	173-178	6	17
β-strand	192-197	6	18
β-strand	202-207	6	18

Chain Y: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	19
β-strand	5	1	20
β-strand	12-14	3	21
β-strand	24	1	20
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	62-63	2	23
β-strand	70	1	20
β-strand	74-75	2	23
β-strand	85-90	6	22
β-strand	95C-95D	2	22
β-strand	96	1	19
β-strand	102-104	3	21
β-strand	112-116	5	24
α-helix	117	1
α-helix	119	1
β-strand	131-137	7	24
β-strand	143-145	3	25
β-strand	158-159	2	24
β-strand	165	1	26
β-strand	169	1	26
β-strand	170-175	6	24
β-strand	190-194	5	25
β-strand	201-203	3	25

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	98	Human gammaherpesvirus 4	P03212 (AlphaFold model)
Soluble gp42	C	protein	33	Human gammaherpesvirus 4	P03205 (AlphaFold model)
769C2 Fab Heavy chain	X	protein	225	Homo sapiens
769C2 Fab Light chain	Y	protein	215	Homo sapiens
769B10 Fab heavy chain	H	protein	234	Homo sapiens
769B10 Fab light chain	L	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>7S07_1 Envelope glycoprotein H (chains A)
ASLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYK
TSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTM
LPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLV
FGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMT
AASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRW
LAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALR
LATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVT
TQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQ
EATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSD
REVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGF
ALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Sequence of entity 2 (B), FASTA

>7S07_2 Envelope glycoprotein L (chains B)
PCCHVTQLAAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVV
SFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLF

Sequence of entity 3 (C), FASTA

>7S07_3 Soluble gp42 (chains C)
KPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLP

Sequence of entity 4 (X), FASTA

>7S07_4 769C2 Fab Heavy chain (chains X)
EVQLVESGGGLVKPGGSLRLSCAASGFTFSTYAMDWVRQAPGKGLEWVSLISSRSSNIYY
SDSVKGNFTISRDNAKNSLFLQMNSLRAEDTAVYYCAREAGGFHSHFDMWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 5 (Y), FASTA

>7S07_5 769C2 Fab Light chain (chains Y)
QSVLTQPASVSGSLGQSVTISCTGTSSDVGGYDYVSWYQQHPGKNPKLMIFEVNNRPSGV
STRFSGSKSGNTASLTISGLQAEDEADYYCNSYSTTTTWVFGGGTSLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Sequence of entity 6 (H), FASTA

>7S07_6 769B10 Fab heavy chain (chains H)
EVQLVESGGGIVQPGGSLRVSCAASGFSLSDHYMDWVRQAPGRGLEWVGRSRNKENSFTT
EFAASVRRRFTISRDDSNSLLHLQMNNLKSEDTAVYFCARVGYYDLWSGYSGNWYIDVWG
RGTLVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGVLTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 7 (L), FASTA

>7S07_7 769B10 Fab light chain (chains L)
DIQMTQSPSSLSASLGDSVTITCRASQTMSNFLNWYQQKPGKAPKFLIYAASRLQSGVPS
RFSGSGSGTQFTLTISNLQPEDFATYYCQQSFLFPYTFGGGTKVEVERTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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…
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…
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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