5W0K: EBV gHgL/CL40/gp42 N-domain

Crystal structure of EBV gHgL/CL40/gp42 N-domain. Determined by X-ray diffraction at 3.1 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Human herpesvirus 4 (strain B95-8), Mus musculus
Chains: 10
Atoms: 18,663
Mol. weight: 273.71 kDa
Released: 4 Oct 2017

Explore 5W0K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W0K contains 96 α-helices and 163 β-strands across 10 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, 31 β-strands

Element	Residues	Length	Sheet
β-strand	22-29	8	1
β-strand	32-39	8	1
α-helix	41-46	6
α-helix	52-58	7
α-helix	65-74	10
β-strand	75	1	2
α-helix	93-96	4
β-strand	100-102	3	3
β-strand	119-122	4	3
α-helix	124-130	7
β-strand	134-136	3	4
α-helix	142-145	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	213-216	4
β-strand	217-221	5	6
β-strand	224-230	7	6
β-strand	231	1	2
α-helix	232-238	7
α-helix	246-255	10
α-helix	258-273	16
α-helix	285-307	23
β-strand	312-314	3	3
α-helix	315-335	21
β-strand	339-341	3	6
α-helix	346-356	11
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-406	15
α-helix	408	1
α-helix	411-414	4
α-helix	415-433	19
α-helix	440-453	14
α-helix	456-467	12
α-helix	471-473	3
α-helix	477-480	4
β-strand	483	1	7
α-helix	488-494	7
α-helix	503-516	14
β-strand	535	1	8
β-strand	541-547	7	7
β-strand	550-555	6	7
β-strand	560	1	8
β-strand	566-567	2	7
β-strand	578-583	6	7
α-helix	591-593	3
α-helix	596	1
β-strand	597	1	7
α-helix	598	1
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 and D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	47-50	4	1
β-strand	61-65	5	1
β-strand	77-81	5	1
α-helix	82-95	14
α-helix	102-117	16
α-helix	120-122	3

Chain C: 29 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	24
β-strand	33-39	7	24
α-helix	40-45	6
α-helix	52-59	8
α-helix	65-74	10
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	134-136	3	27
β-strand	148	1	28
β-strand	152-154	3	27
β-strand	156	1	29
β-strand	158-162	5	29
β-strand	167-173	7	29
β-strand	177-185	9	29
β-strand	191-200	10	29
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	232-238	7
α-helix	246-255	10
α-helix	258-272	15
α-helix	285-306	22
β-strand	312-314	3	26
α-helix	315-335	21
β-strand	339-340	2	29
α-helix	346-356	11
α-helix	361-366	6
α-helix	369-382	14
α-helix	392-406	15
α-helix	408	1
α-helix	411-414	4
α-helix	415-433	19
α-helix	440-453	14
α-helix	456-467	12
α-helix	471-473	3
α-helix	477-480	4
β-strand	483	1	30
α-helix	488-494	7
α-helix	503-516	14
β-strand	535	1	31
β-strand	541-547	7	30
β-strand	550-555	6	30
β-strand	560	1	31
β-strand	566-567	2	30
β-strand	578-583	6	30
α-helix	591-593	3
α-helix	596	1
β-strand	597	1	30
α-helix	598	1
β-strand	601-602	2	32
β-strand	618-623	6	32
β-strand	627-633	7	32
α-helix	637-645	9
β-strand	656-661	6	32
β-strand	667-670	4	32

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	33
β-strand	9-12	4	34
β-strand	18-20	3	33
β-strand	23-25	3	33
β-strand	27	1	17
α-helix	29-31	3
β-strand	33-39	7	34
β-strand	45-51	7	34
β-strand	58-60	3	34
β-strand	70-73	4	33
β-strand	78-83	6	33
α-helix	88-90	3
β-strand	92-99	8	34
β-strand	106	1	34
α-helix	107-109	3
β-strand	110-114	5	34
β-strand	120	1	35
β-strand	123-127	5	36
β-strand	138-148	11	36
β-strand	149	1	35
β-strand	154-157	4	37
β-strand	166-168	3	36
α-helix	169-171	3
β-strand	172-174	3	36
β-strand	177-187	11	36
β-strand	194	1	13
β-strand	197-202	6	37
β-strand	207-212	6	37

Chain F: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	38
β-strand	10-13	4	39
β-strand	19-25	7	38
β-strand	33-38	6	39
β-strand	45-49	5	39
β-strand	53-54	2	39
α-helix	55	1
β-strand	62-67	6	38
β-strand	70-75	6	38
α-helix	80-82	3
β-strand	85-90	6	39
α-helix	96	1
β-strand	97-98	2	39
β-strand	102-106	5	39
β-strand	114-118	5	40
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	40
β-strand	145-148	4	41
β-strand	150	1	42
β-strand	153	1	42
α-helix	154-155	2
β-strand	159-163	5	40
α-helix	164-167	4
β-strand	173-182	10	40
α-helix	183-188	6
β-strand	191-197	7	41
α-helix	204	1
β-strand	205-210	6	41

Chain H: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	10
β-strand	9-11	3	11
β-strand	18	1	12
β-strand	21-25	5	10
β-strand	27	1	13
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-52	8	11
β-strand	57-59	3	11
β-strand	70-73	4	10
β-strand	78-81	4	10
β-strand	83	1	12
α-helix	88-90	3
β-strand	93-99	7	11
β-strand	103-106	4	11
β-strand	110-113	4	11
α-helix	117-119	3
β-strand	120	1	14
β-strand	123-127	5	15
β-strand	138-148	11	15
β-strand	149	1	14
β-strand	154-157	4	16
β-strand	166-168	3	15
α-helix	169-171	3
β-strand	172-174	3	15
β-strand	177-187	11	15
β-strand	194	1	17
β-strand	196	1	18
β-strand	198-202	5	16
β-strand	207-210	4	16
β-strand	213	1	18

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	19
β-strand	10-13	4	20
β-strand	19-25	7	19
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	85-90	6	20
α-helix	96	1
β-strand	97-98	2	20
β-strand	102-106	5	20
β-strand	111	1	21
β-strand	114-118	5	22
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	22
β-strand	140	1	21
β-strand	145-150	6	23
β-strand	153	1	23
α-helix	154-155	2
β-strand	159-163	5	22
α-helix	164-167	4
β-strand	173-182	10	22
α-helix	183-188	6
β-strand	192-197	6	23
α-helix	204	1
β-strand	205-209	5	23

Chain X: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	52-54	3
α-helix	56-61	6
β-strand	75	1	4

1 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	A, C	protein	660	Human herpesvirus 4 (strain B95-8)	P03231 (AlphaFold model)
Envelope glycoprotein L	B, D	protein	114	Human herpesvirus 4 (strain B95-8)	P03212 (AlphaFold model)
CL40 IgG heavy chain	E, H	protein	217	Mus musculus
CL40 IgG light chain	F, L	protein	213	Mus musculus
Glycoprotein 42	X, Y	protein	35	Human herpesvirus 4 (strain B95-8)	P03205 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5W0K_1 Envelope glycoprotein H (chains A, C)
LSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTS
GTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLP
NTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFG
KTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAA
SYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLA
KSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLA
TVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQ
GPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEA
TLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDRE
VRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFAL
LSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLYEERAH

Sequence of entity 2 (B, D), FASTA

>5W0K_2 Envelope glycoprotein L (chains B, D)
WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGL
NVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHRGG

Sequence of entity 3 (E, H), FASTA

>5W0K_3 CL40 IgG heavy chain (chains E, H)
EVKLQQSGAELVMPGASVKMSCKASGYTFTDYWMHWVKQRPGQGLEWIGAIDTSDSYTSY
NQKFKGKATLTVDESSSTAYMQLSSLTSEDSAVYYCARGLLPFDYWGQGTTLTVSSAKTT
PPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 4 (F, L), FASTA

>5W0K_4 CL40 IgG light chain (chains F, L)
DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPD
RFTGSGSGTDFTLTISNVQSEDLAKYFCQQYNSYPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 5 (X, Y), FASTA

>5W0K_5 Glycoprotein 42 (chains X, Y)
KPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHW

Primary citation

Inhibition of EBV-mediated membrane fusion by anti-gHgL antibodies. Sathiyamoorthy, K., Jiang, J., Mohl, B.S. et al. Proc Natl Acad Sci U S A (2017) 114:E8703-E8710. DOI 10.1073/pnas.1704661114 · 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
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…

Browse structure collections

About this viewer

MolViewer shows 5W0K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.