3PHF: Epstein-Barr virus gH and gL complex

Crystal Structure of the Epstein-Barr virus gH and gL complex. Determined by X-ray diffraction at 3.58 Å resolution. Released 12 Jan 2011.

Method: X-ray diffraction
Resolution: 3.58 Å
Organism: Human herpesvirus 4
Chains: 32
Atoms: 94,656
Mol. weight: 1347.94 kDa
Released: 12 Jan 2011

Explore 3PHF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PHF contains 553 α-helices and 524 β-strands across 32 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 1: 30 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	8
β-strand	33-37	5	8
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-68	4
α-helix	70-73	4
β-strand	82-83	2	9
α-helix	93-96	4
β-strand	102	1	10
β-strand	120-122	3	10
α-helix	123-130	8
β-strand	134	1	11
α-helix	142-147	6
β-strand	148	1	12
β-strand	154	1	11
β-strand	156-162	7	9
β-strand	167-173	7	9
β-strand	177-185	9	9
β-strand	191-200	10	9
α-helix	201-203	3
α-helix	204-206	3
β-strand	207	1	12
α-helix	213-216	4
β-strand	217-220	4	9
β-strand	224-230	7	9
α-helix	232-239	8
α-helix	246-252	7
α-helix	258-274	17
α-helix	285-307	23
β-strand	312-314	3	10
α-helix	315-335	21
β-strand	339-341	3	9
α-helix	346-357	12
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-405	14
α-helix	416-433	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	477-480	4
β-strand	483	1	13
α-helix	488-494	7
α-helix	503-520	18
α-helix	530-534	5
α-helix	538-540	3
β-strand	541-546	6	13
β-strand	550-555	6	13
β-strand	566-567	2	13
β-strand	570	1	85
β-strand	578-583	6	13
α-helix	587-588	2
α-helix	596	1
β-strand	597-598	2	13
β-strand	601-602	2	14
β-strand	618-623	6	14
β-strand	628-633	6	14
α-helix	637-644	8
β-strand	656-661	6	14
β-strand	667-670	4	14

Chain 2: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
β-strand	47-50	4	8
β-strand	61-67	7	8
β-strand	75-81	7	8
α-helix	82-94	13
α-helix	97-99	3
α-helix	103-115	13
α-helix	120-125	6

Chain 3: 31 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	24
β-strand	36-38	3	24
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-68	4
α-helix	70-73	4
β-strand	75	1	25
β-strand	82-83	2	26
α-helix	87-90	4
α-helix	93-95	3
β-strand	120-122	3	27
α-helix	123-130	8
β-strand	134	1	28
α-helix	142-147	6
β-strand	148	1	29
β-strand	154	1	28
β-strand	156-162	7	26
β-strand	167-173	7	26
β-strand	177-185	9	26
β-strand	191-200	10	26
α-helix	201-203	3
α-helix	204-206	3
β-strand	207	1	29
α-helix	213-216	4
β-strand	217-220	4	26
β-strand	224-230	7	26
β-strand	231	1	25
α-helix	232-239	8
α-helix	246-252	7
α-helix	258-274	17
α-helix	285-307	23
β-strand	312-314	3	27
α-helix	315-335	21
β-strand	339-341	3	26
α-helix	346-357	12
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-405	14
α-helix	416-433	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	477-480	4
β-strand	483	1	30
α-helix	488-494	7
α-helix	503-520	18
α-helix	530-534	5
α-helix	538-540	3
β-strand	541-546	6	30
β-strand	550-555	6	30
β-strand	566-567	2	30
β-strand	578-583	6	30
α-helix	587-588	2
α-helix	596	1
β-strand	597-598	2	30
β-strand	601-602	2	31
β-strand	618-623	6	31
β-strand	628-633	6	31
α-helix	637-644	8
β-strand	656-661	6	31
β-strand	667-670	4	31

Chains 4, 6, B, D and T: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	47-50	4	24
β-strand	61-67	7	24
β-strand	75-81	7	24
α-helix	82-94	13
α-helix	97-99	3
α-helix	103-115	13
α-helix	120-122	3

Chain 5: 31 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	41
β-strand	36-38	3	41
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-68	4
α-helix	69-71	3
β-strand	75	1	42
β-strand	82-83	2	43
α-helix	94-96	3
β-strand	101-102	2	44
β-strand	120-122	3	44
α-helix	123-130	8
β-strand	134	1	45
α-helix	142-147	6
β-strand	148	1	46
β-strand	154	1	45
β-strand	156-162	7	43
β-strand	167-173	7	43
β-strand	177-185	9	43
β-strand	191-200	10	43
α-helix	201-203	3
α-helix	204-206	3
β-strand	207	1	46
α-helix	213-216	4
β-strand	217-220	4	43
β-strand	224-230	7	43
β-strand	231	1	42
α-helix	232-239	8
α-helix	246-252	7
α-helix	258-274	17
α-helix	285-307	23
β-strand	312-314	3	44
α-helix	315-335	21
β-strand	339-341	3	43
α-helix	346-356	11
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-405	14
α-helix	416-433	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	477-480	4
β-strand	483	1	47
α-helix	488-494	7
α-helix	503-520	18
α-helix	524-526	3
α-helix	530-534	5
α-helix	538-540	3
β-strand	541-546	6	47
β-strand	550-555	6	47
β-strand	566-567	2	47
β-strand	578-583	6	47
α-helix	587-588	2
α-helix	596	1
β-strand	597-598	2	47
β-strand	601-602	2	48
β-strand	618-623	6	48
β-strand	628-633	6	48
α-helix	637-644	8
β-strand	656-661	6	48
β-strand	667-670	4	48

Chain A: 30 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	1
β-strand	35-37	3	1
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-73	9
β-strand	82-83	2	2
α-helix	87-90	4
α-helix	93-94	2
β-strand	100-102	3	3
β-strand	119-122	4	3
α-helix	123-130	8
β-strand	134	1	4
α-helix	142-147	6
β-strand	148	1	5
β-strand	154	1	4
β-strand	156-162	7	2
β-strand	167-173	7	2
β-strand	177-185	9	2
β-strand	191-200	10	2
α-helix	201-203	3
β-strand	207	1	5
α-helix	213-215	3
β-strand	217-220	4	2
β-strand	224-230	7	2
α-helix	232-239	8
α-helix	246-252	7
α-helix	258-274	17
α-helix	285-307	23
β-strand	312-314	3	3
α-helix	315-335	21
β-strand	339-341	3	2
α-helix	346-356	11
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-405	14
α-helix	416-433	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	477-480	4
β-strand	483	1	6
α-helix	488-494	7
α-helix	503-520	18
α-helix	524-526	3
α-helix	530-534	5
α-helix	538-540	3
β-strand	541-546	6	6
β-strand	550-555	6	6
β-strand	566-567	2	6
β-strand	578-583	6	6
α-helix	587-588	2
α-helix	596	1
β-strand	597-598	2	6
β-strand	601-602	2	7
β-strand	618-623	6	7
β-strand	628-633	6	7
α-helix	637-644	8
β-strand	656-661	6	7
β-strand	667-670	4	7

Chain C: 32 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	15
β-strand	28	1	16
β-strand	33	1	16
α-helix	34	1
β-strand	36-38	3	15
α-helix	40-46	7
α-helix	52-58	7
α-helix	65-73	9
β-strand	75	1	17
β-strand	82-83	2	18
α-helix	93-94	2
α-helix	99	1
β-strand	100-102	3	19
β-strand	119-122	4	19
α-helix	123-130	8
β-strand	134	1	20
α-helix	142-147	6
β-strand	148	1	21
β-strand	154	1	20
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	204-206	3
β-strand	207	1	21
α-helix	213-215	3
β-strand	217-220	4	18
β-strand	224-230	7	18
β-strand	231	1	17
α-helix	232-239	8
α-helix	246-251	6
α-helix	258-274	17
α-helix	285-307	23
β-strand	312-314	3	19
α-helix	315-335	21
β-strand	339-341	3	18
α-helix	346-357	12
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-405	14
α-helix	416-433	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	477-480	4
β-strand	483	1	22
α-helix	488-494	7
α-helix	503-520	18
α-helix	524-526	3
α-helix	530-534	5
α-helix	538-540	3
β-strand	541-546	6	22
β-strand	550-555	6	22
β-strand	566-567	2	22
β-strand	578-583	6	22
α-helix	587-588	2
α-helix	596	1
β-strand	597-598	2	22
β-strand	601-602	2	23
β-strand	618-623	6	23
β-strand	628-633	6	23
α-helix	637-644	8
β-strand	656-661	6	23
β-strand	667-670	4	23

Chain E: 31 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	32
α-helix	33-34	2
β-strand	35-37	3	32
α-helix	40-46	7
α-helix	52-58	7
α-helix	68-72	5
β-strand	75	1	33
α-helix	87-90	4
α-helix	99	1
β-strand	100-102	3	34
β-strand	103	1	35
β-strand	106	1	35
β-strand	119-122	4	34
α-helix	123-130	8
β-strand	134	1	36
α-helix	142-147	6
β-strand	148	1	37
β-strand	154	1	36
β-strand	156-162	7	38
β-strand	167-173	7	38
β-strand	177-185	9	38
β-strand	191-200	10	38
α-helix	201-203	3
β-strand	207	1	37
α-helix	213-215	3
β-strand	217-220	4	38
β-strand	224-230	7	38
β-strand	231	1	33
α-helix	232-239	8
α-helix	246-252	7
α-helix	258-274	17
α-helix	285-307	23
β-strand	312-314	3	34
α-helix	315-335	21
β-strand	339-341	3	38
α-helix	346-356	11
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-405	14
α-helix	416-433	18
α-helix	440-453	14
α-helix	456-468	13
α-helix	477-480	4
β-strand	483	1	39
α-helix	488-494	7
α-helix	503-520	18
α-helix	525-527	3
α-helix	530-534	5
α-helix	538-540	3
β-strand	541-546	6	39
β-strand	550-555	6	39
β-strand	566-567	2	39
β-strand	578-583	6	39
α-helix	587-588	2
α-helix	596	1
β-strand	597-598	2	39
β-strand	601-602	2	40
β-strand	618-623	6	40
β-strand	628-633	6	40
α-helix	637-644	8
β-strand	656-661	6	40
β-strand	667-670	4	40

15 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	1, 3, 5, A, C, E, G, I, K, M, O, Q, S, U, W, Y	protein	653	Human herpesvirus 4	P03231 (AlphaFold model)
Envelope glycoprotein L	2, 4, 6, B, D, F, H, J, L, N, P, R, T, V, X, Z	protein	108	Human herpesvirus 4	P03212 (AlphaFold model)

Sequence of entity 1 (1, 3, 5, A, C, E, G, I, K, M, O, Q, S, U, W, Y), FASTA

>3PHF_1 Envelope glycoprotein H (chains 1, 3, 5, A, C, E, G, I, K, M, O, Q, S, U, W, Y)
LSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTS
GTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLP
NTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFG
KTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAA
SYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLA
KSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLA
TVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQ
GPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEA
TLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDRE
VRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFAL
LSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAG

Sequence of entity 2 (2, 4, 6, B, D, F, H, J, L, N, P, R, T, V, X, Z), FASTA

>3PHF_2 Envelope glycoprotein L (chains 2, 4, 6, B, D, F, H, J, L, N, P, R, T, V, X, Z)
WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGL
NVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRY

Primary citation

Crystal structure of the Epstein-Barr virus (EBV) glycoprotein H/glycoprotein L (gH/gL) complex. Matsuura, H., Kirschner, A.N., Longnecker, R. et al. Proc Natl Acad Sci U S A (2010) 107:22641-22646. DOI 10.1073/pnas.1011806108 · 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…
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)
6C5V 4.8 Å, An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of…

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