5T1D: EBV gHgL/gp42/E1D1 complex

Crystal structure of EBV gHgL/gp42/E1D1 complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 28 Dec 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Epstein-Barr virus (strain B95-8), Epstein-Barr virus (strain GD1), Mus musculus
Chains: 5
Atoms: 10,617
Mol. weight: 154.38 kDa
Released: 28 Dec 2016

Explore 5T1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5T1D contains 48 α-helices and 89 β-strands across 5 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: 29 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	22-27	6	1
β-strand	35-39	5	1
α-helix	54-59	6
α-helix	65-72	8
β-strand	75	1	2
α-helix	93-95	3
β-strand	100-102	3	3
α-helix	104-106	3
β-strand	119-122	4	3
α-helix	123-130	8
β-strand	134-136	3	4
α-helix	144-147	4
β-strand	148	1	5
β-strand	152-154	3	4
β-strand	156-162	7	6
β-strand	167-173	7	6
β-strand	177-185	9	6
β-strand	191-200	10	6
α-helix	205-206	2
β-strand	207	1	5
α-helix	208	1
β-strand	217-220	4	6
β-strand	224-229	6	6
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	3
α-helix	315-336	22
β-strand	339-341	3	6
α-helix	346-355	10
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-406	15
α-helix	408	1
α-helix	415-433	19
α-helix	440-452	13
α-helix	456-468	13
α-helix	471-473	3
β-strand	483	1	7
α-helix	488-493	6
α-helix	503-516	14
α-helix	530-534	5
α-helix	538-540	3
β-strand	541-547	7	7
β-strand	550-555	6	7
β-strand	566-567	2	7
β-strand	578-583	6	7
α-helix	596	1
β-strand	597	1	7
α-helix	598-600	3
β-strand	601-602	2	8
β-strand	618-623	6	8
β-strand	627-633	7	8
α-helix	637-645	9
β-strand	656-661	6	8
β-strand	667-670	4	8

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	47-50	4	1
β-strand	61-65	5	1
β-strand	75-81	7	1
α-helix	82-95	14
α-helix	97-99	3
α-helix	103-117	15

Chain C: 6 helices, 14 β-strands

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	4
β-strand	109-111	3	9
β-strand	114-118	5	9
β-strand	123	1	10
α-helix	128-133	6
β-strand	140-141	2	9
α-helix	149-154	6
β-strand	162-163	2	11
β-strand	167	1	12
β-strand	175	1	12
β-strand	185	1	11
β-strand	193-195	3	11
β-strand	203-204	2	11
β-strand	212	1	10
β-strand	214	1	11
β-strand	215-218	4	9

Chain H: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-20	3	15
β-strand	22-26	5	13
β-strand	27-29	3	1
β-strand	34-39	6	14
β-strand	49-51	3	14
β-strand	58-59	2	14
β-strand	69-70	2	15
β-strand	81-83	3	15
β-strand	92-98	7	14
β-strand	104-105	2	14
β-strand	109-113	5	14
β-strand	119	1	16
α-helix	120-121	2
β-strand	122-126	5	17
β-strand	137-147	11	17
β-strand	148	1	16
β-strand	153-156	4	18
β-strand	165-167	3	17
α-helix	168-170	3
β-strand	171-173	3	17
β-strand	176-186	11	17
α-helix	187-189	3
β-strand	196-200	5	18
β-strand	206-210	5	18

Chain L: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	18-25	8	19
β-strand	38-43	6	20
β-strand	50-54	5	20
β-strand	58-59	2	20
α-helix	60	1
β-strand	67-72	6	19
β-strand	75-81	7	19
α-helix	85-87	3
β-strand	89-95	7	20
β-strand	108-111	4	20
β-strand	116	1	21
β-strand	119-123	5	22
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	22
β-strand	145	1	21
β-strand	150-155	6	23
β-strand	158-160	3	23
β-strand	164-168	5	22
α-helix	169-172	4
β-strand	178-187	10	22
α-helix	188-191	4
β-strand	196-202	7	23
β-strand	210-215	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A	protein	655	Epstein-Barr virus (strain B95-8)	P03231 (AlphaFold model)
Envelope glycoprotein L	B	protein	112	Epstein-Barr virus (strain B95-8)	P03212 (AlphaFold model)
Glycoprotein 42	C	protein	191	Epstein-Barr virus (strain GD1)	P0C6Z5
E1D1 IgG2a heavy chain	H	protein	213	Mus musculus
E1D1 IgG2a light chain	L	protein	217	Mus musculus

Sequence of entity 1 (A), FASTA

>5T1D_1 Envelope glycoprotein H (chains A)
LSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTS
GTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLP
NTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFG
KTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAA
SYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLA
KSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLA
TVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQ
GPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEA
TLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDRE
VRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFAL
LSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Sequence of entity 2 (B), FASTA

>5T1D_2 Envelope glycoprotein L (chains B)
WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGL
NVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHR

Sequence of entity 3 (C), FASTA

>5T1D_3 Glycoprotein 42 (chains C)
GGGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHWTPTLHTFQVPQ
NYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVV
TRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLK
PCLCVSQRSNS

Sequence of entity 4 (H), FASTA

>5T1D_4 E1D1 IgG2a heavy chain (chains H)
EVQLEQSGPELVKPGASVKMSCKASGYTFTDYVISWVKQRTGQGLEWIGEIYPESGNTYY
NEKFKGEATLTADKSSNTAYMQLSRLTSEDSAVYFCAEGYAMDFWGQGTSVTVSSAKTTP
PSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLS
SSVTVPSSTWPSETVTCNVAHPASSTKVDKKIV

Sequence of entity 5 (L), FASTA

>5T1D_5 E1D1 IgG2a light chain (chains L)
DIVITQTPLSLPVSLGDQASISCRSSQSLLHSNGNTYLHWYLQRPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLMINRVEAEDLGVYFCSQSIHVPRTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Primary citation

Structural basis for Epstein-Barr virus host cell tropism mediated by gp42 and gHgL entry glycoproteins. Sathiyamoorthy, K., Hu, Y.X., Mohl, B.S. et al. Nat Commun (2016) 7:13557-13557. DOI 10.1038/ncomms13557 · 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…
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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