7CZE: Epstein-Barr virus (EBV) gHgL and

Crystal structure of Epstein-Barr virus (EBV) gHgL and in complex with the ligand binding domian (LBD) of EphA2. Determined by X-ray diffraction at 3.0 Å resolution. Released 21 Oct 2020.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Epstein-Barr virus (strain B95-8), Human herpesvirus 4 strain B95-8, Homo sapiens
Chains: 12
Atoms: 29,320
Mol. weight: 431.84 kDa
Ligands: NAG
Released: 21 Oct 2020

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

Secondary structure: helices and β-sheets

7CZE contains 128 α-helices and 203 β-strands across 12 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: 28 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	22-29	8	1
β-strand	32-39	8	1
α-helix	40-46	7
β-strand	48	1	2
β-strand	50	1	2
α-helix	52-58	7
α-helix	65-72	8
β-strand	75	1	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	135-138	4	5
β-strand	148	1	6
β-strand	151-153	3	5
β-strand	156-162	7	7
β-strand	167-173	7	7
β-strand	177-185	9	7
β-strand	191-200	10	7
α-helix	201-203	3
α-helix	205-206	2
β-strand	207	1	6
α-helix	213-216	4
β-strand	217-221	5	7
β-strand	224-230	7	7
β-strand	231	1	3
α-helix	232-239	8
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	7
α-helix	346-356	11
α-helix	361-363	3
α-helix	371-381	11
α-helix	383-385	3
α-helix	392-405	14
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	477-480	4
β-strand	483	1	8
α-helix	488-492	5
α-helix	503-515	13
β-strand	541-547	7	8
β-strand	550-555	6	8
β-strand	566-567	2	8
β-strand	578-583	6	8
α-helix	591-593	3
β-strand	597	1	8
β-strand	601-602	2	9
β-strand	618-623	6	9
β-strand	627-633	7	9
α-helix	637-645	9
β-strand	656-661	6	9
β-strand	667-670	4	9

Chains B, D, F and H: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	47-50	4	1
β-strand	61-65	5	1
β-strand	69	1	10
β-strand	74	1	10
β-strand	75-76	2	11
β-strand	77-81	5	1
α-helix	82-95	14
α-helix	102-117	16

Chain C: 29 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	22-29	8	12
β-strand	32-39	8	12
α-helix	40-46	7
β-strand	48	1	13
β-strand	50	1	13
α-helix	52-58	7
α-helix	65-72	8
β-strand	75	1	14
α-helix	93-96	4
β-strand	100-102	3	15
β-strand	119-122	4	15
α-helix	123-130	8
β-strand	135-138	4	16
β-strand	148	1	17
β-strand	151-153	3	16
β-strand	156-162	7	18
β-strand	167-173	7	18
β-strand	177-185	9	18
β-strand	191-200	10	18
α-helix	201-203	3
α-helix	205-206	2
β-strand	207	1	17
α-helix	213-216	4
β-strand	217-221	5	18
β-strand	224-230	7	18
β-strand	231	1	14
α-helix	232-239	8
α-helix	246-255	10
α-helix	258-274	17
α-helix	285-306	22
β-strand	312-314	3	15
α-helix	315-335	21
β-strand	339-341	3	18
α-helix	346-356	11
α-helix	361-366	6
α-helix	371-381	11
α-helix	383-385	3
α-helix	392-405	14
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	477-480	4
β-strand	483	1	19
α-helix	488-492	5
α-helix	503-515	13
α-helix	538-540	3
β-strand	541-547	7	19
β-strand	550-555	6	19
β-strand	566-567	2	19
β-strand	578-583	6	19
α-helix	591-593	3
β-strand	597	1	19
β-strand	601-602	2	20
β-strand	618-623	6	21
β-strand	627-633	7	21
α-helix	637-645	9
β-strand	656-657	2	21
β-strand	658	1	20
β-strand	660-661	2	21
β-strand	667	1	21
β-strand	669-670	2	20

Chain E: 28 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	22-29	8	24
β-strand	32-39	8	24
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-72	8
β-strand	75	1	25
α-helix	93-96	4
β-strand	100-102	3	26
β-strand	119-122	4	26
α-helix	123-130	8
β-strand	134-138	5	27
β-strand	148	1	28
β-strand	151-154	4	27
β-strand	156-162	7	29
β-strand	167-173	7	29
β-strand	177-185	9	29
β-strand	191-200	10	29
α-helix	201-203	3
α-helix	205-206	2
β-strand	207	1	28
α-helix	213-216	4
β-strand	217-221	5	29
β-strand	224-230	7	29
β-strand	231	1	25
α-helix	232-239	8
α-helix	246-255	10
α-helix	258-274	17
α-helix	285-306	22
β-strand	312-314	3	26
α-helix	315-335	21
β-strand	339-341	3	29
α-helix	346-356	11
α-helix	361-363	3
α-helix	371-381	11
α-helix	392-405	14
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	477-480	4
β-strand	483	1	30
α-helix	488-492	5
α-helix	503-515	13
α-helix	538-540	3
β-strand	541-547	7	30
β-strand	550-555	6	30
β-strand	566-567	2	30
β-strand	578-583	6	30
α-helix	591-593	3
β-strand	597	1	30
β-strand	601-602	2	31
β-strand	618-623	6	31
β-strand	627-633	7	31
α-helix	637-645	9
β-strand	656-661	6	31
β-strand	667-670	4	31

Chain G: 27 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	22-29	8	34
β-strand	32-39	8	34
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-72	8
β-strand	75	1	35
α-helix	93-96	4
β-strand	100-102	3	36
β-strand	119-122	4	36
α-helix	123-130	8
β-strand	134-138	5	37
β-strand	148	1	38
β-strand	151-154	4	37
β-strand	156-162	7	39
β-strand	167-173	7	39
β-strand	177-185	9	39
β-strand	191-200	10	39
α-helix	201-203	3
α-helix	205-206	2
β-strand	207	1	38
α-helix	213-216	4
β-strand	217-221	5	39
β-strand	224-230	7	39
β-strand	231	1	35
α-helix	232-239	8
α-helix	246-255	10
α-helix	258-274	17
α-helix	285-306	22
β-strand	312-314	3	36
α-helix	315-335	21
β-strand	339-341	3	39
α-helix	346-356	11
α-helix	361-366	6
α-helix	371-381	11
α-helix	392-405	14
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	477-480	4
β-strand	483	1	40
α-helix	488-492	5
α-helix	503-515	13
β-strand	541-547	7	40
β-strand	550-555	6	40
β-strand	566-567	2	40
β-strand	578-583	6	40
α-helix	591-593	3
β-strand	597	1	40
β-strand	601-602	2	41
β-strand	618-623	6	41
β-strand	627-633	7	41
α-helix	637-645	9
β-strand	656-661	6	41
β-strand	667-670	4	41

Chains I, J, K and L: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	11
β-strand	44-46	3	44
β-strand	53-58	6	11
β-strand	63-70	8	11
β-strand	79-82	4	44
β-strand	86-87	2	44
β-strand	94-102	9	11
β-strand	116	1	45
β-strand	119-126	8	44
α-helix	136-138	3
α-helix	139	1
β-strand	140-145	6	44
β-strand	164-170	7	11
β-strand	177-184	8	44
β-strand	187	1	45
β-strand	188-199	12	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein H	A, C, E, G	protein	662	Epstein-Barr virus (strain B95-8)	P03231 (AlphaFold model)
Envelope glycoprotein L	B, D, F, H	protein	114	Human herpesvirus 4 strain B95-8	P03212 (AlphaFold model)
Ephrin type-A receptor 2	I, J, K, L	protein	183	Homo sapiens	P29317 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>7CZE_1 Envelope glycoprotein H (chains A, C, E, G)
ASLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYK
TSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTM
LPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLV
FGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMT
AASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRW
LAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALR
LATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVT
TQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQ
EATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSD
REVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGF
ALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLYEER
AH

Sequence of entity 2 (B, D, F, H), FASTA

>7CZE_2 Envelope glycoprotein L (chains B, D, F, H)
WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGL
NVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHRGG

Sequence of entity 3 (I, J, K, L), FASTA

>7CZE_3 Ephrin type-A receptor 2 (chains I, J, K, L)
GKEVVLLDFAAAGGELGWLTHPYGKGWDLMQNIMNDMPIYMYSVCNVMSGDQDNWLRTNW
VYRGEAERIFIELKFTVRDCNSFPGGASSCKETFNLYYAESDLDYGTNFQKRLFTKIDTI
APDEITVSSDFEARHVKLNVEERSVGPLTRKGFYLAFQDIGACVALLSVRVYYKKHHHHH
HHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16

Primary citation

Molecular basis of EphA2 recognition by gHgL from gammaherpesviruses. Su, C., Wu, L., Chai, Y. et al. Nat Commun (2020) 11:5964-5964. DOI 10.1038/s41467-020-19617-9 · PubMed

Other PDB entries of the same protein (UniProt P03231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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…
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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