1KG0: Epstein-Barr Virus gp42 Protein

Structure of the Epstein-Barr Virus gp42 Protein Bound to the MHC class II Receptor HLA-DR1. Determined by X-ray diffraction at 2.65 Å resolution. Released 27 Mar 2002.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Homo sapiens, synthetic construct, Human herpesvirus 4
Chains: 4
Atoms: 4,844
Mol. weight: 59.96 kDa
Released: 27 Mar 2002

Explore 1KG0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1KG0 contains 13 α-helices and 46 β-strands across 4 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: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-49	4
β-strand	53	1	2
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-127	2	5
β-strand	133-134	2	4
α-helix	137	1
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-61	7
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-87	7
β-strand	95	1	6
β-strand	98-103	6	7
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-138	3	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain C: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	100	1	9
β-strand	109-111	3	9
β-strand	114-118	5	9
β-strand	123	1	10
α-helix	127-135	9
β-strand	140-141	2	9
α-helix	149-154	6
β-strand	162-163	2	11
β-strand	166-168	3	12
β-strand	174-176	3	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	215-219	5	9

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	307	1	2
α-helix	308-317	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class II Receptor HLA-DR1	A	protein	180	Homo sapiens	P01903 (AlphaFold model)
MHC class II Receptor HLA-DR1	B	protein	188	Homo sapiens	P01911 (AlphaFold model)
Hemagglutinin HA Peptide	D	protein	13	synthetic construct	P03437
gp42 Protein	C	protein	136	Human herpesvirus 4	P03205 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1KG0_1 MHC class II Receptor HLA-DR1 (chains A)
EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALAN
IAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWL
RNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDA

Sequence of entity 2 (B), FASTA

>1KG0_2 MHC class II Receptor HLA-DR1 (chains B)
TRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWN
SQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGF
YPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTS
PLTVEWRA

Sequence of entity 3 (D), FASTA

>1KG0_3 Hemagglutinin HA Peptide (chains D)
PKYVKQNTLKLAT

Sequence of entity 4 (C), FASTA

>1KG0_4 gp42 Protein (chains C)
HTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPT
PDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSH
HECSFLKPCLCVSQRS

Primary citation

Structure of the Epstein-Barr virus gp42 protein bound to the MHC class II receptor HLA-DR1. Mullen, M.M., Haan, K.M., Longnecker, R. et al. Mol Cell (2002) 9:375-385. DOI 10.1016/S1097-2765(02)00465-3 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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