2VIR: Influenza virus hemagglutinin

Influenza virus hemagglutinin complexed with a neutralizing antibody. Determined by X-ray diffraction at 3.25 Å resolution. Released 29 Apr 1998.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Mus musculus, Influenza A virus (A/X-31(H3N2))
Chains: 3
Atoms: 5,339
Mol. weight: 77.74 kDa
Ligands: ZN
Released: 29 Apr 1998

Explore 2VIR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VIR contains 19 α-helices and 80 β-strands across 3 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: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-12	4	2
β-strand	17-22	6	3
β-strand	23-24	2	1
β-strand	27	1	1
α-helix	31-33	3
β-strand	36-41	6	2
β-strand	45-51	7	2
β-strand	55-56	2	2
β-strand	64-69	6	3
β-strand	72-78	7	3
α-helix	82-84	3
β-strand	86-93	8	2
β-strand	98-100	3	2
β-strand	101	1	1
β-strand	105-108	4	2
β-strand	114	1	4
β-strand	117	1	5
β-strand	120-121	2	5
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	5
β-strand	143	1	4
β-strand	148-153	6	6
β-strand	156-157	2	6
α-helix	158	1
β-strand	162-164	3	5
α-helix	165-167	3
β-strand	168-169	2	5
β-strand	175-183	9	5
α-helix	185-189	5
β-strand	194-200	7	6
β-strand	203-209	7	6

Chain B: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	17-25	9	7
β-strand	33-39	7	9
β-strand	46-51	6	9
β-strand	57-59	3	9
α-helix	63-65	3
β-strand	67-72	6	7
β-strand	77-83	7	7
α-helix	87-89	3
β-strand	91-100	10	9
β-strand	107-112	6	9
β-strand	116-118	3	9
β-strand	119-120	2	8
β-strand	126	1	10
α-helix	127-128	2
β-strand	129-133	5	11
β-strand	144-154	11	11
β-strand	155	1	10
β-strand	160-163	4	12
α-helix	164-166	3
β-strand	168	1	12
β-strand	174	1	11
α-helix	175-177	3
β-strand	178-180	3	11
β-strand	183-193	11	11
β-strand	203-208	6	12
α-helix	209-211	3
β-strand	213-218	6	12

Chain C: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	44	1	13
β-strand	51-54	4	14
β-strand	58-60	3	15
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	16
β-strand	86-89	4	15
β-strand	100-101	2	17
α-helix	105-115	11
β-strand	117	1	16
β-strand	120-122	3	17
β-strand	131-134	4	17
β-strand	136-141	6	18
β-strand	144-146	3	18
β-strand	151-155	5	17
β-strand	157	1	19
β-strand	160	1	19
β-strand	165-170	6	20
β-strand	176-184	9	17
α-helix	188-195	8
β-strand	202-205	4	20
β-strand	211-213	3	20
α-helix	220-222	3
β-strand	223	1	21
β-strand	226	1	21
β-strand	229-237	9	17
β-strand	241-247	7	20
β-strand	251-254	4	17
β-strand	256-259	4	17
β-strand	266-269	4	15
β-strand	274-278	5	14
β-strand	282-283	2	22
β-strand	286-287	2	22
β-strand	294-295	2	13
β-strand	302	1	22
α-helix	306	1
β-strand	307-308	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin (IgG1, lambda)	A	protein	210	Mus musculus	G0YP42 (AlphaFold model)
Immunoglobulin (IgG1, lambda)	B	protein	221	Mus musculus	P01868 (AlphaFold model)
Hemagglutinin	C	protein	282	Influenza A virus (A/X-31(H3N2))	P03438

Sequence of entity 1 (A), FASTA

>2VIR_1 IMMUNOGLOBULIN (IGG1, LAMBDA) (chains A)
QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTL
FPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSY
LTLTARAWERHSSYSCQVTHEGHTVEKSLS

Sequence of entity 2 (B), FASTA

>2VIR_2 IMMUNOGLOBULIN (IGG1, LAMBDA) (chains B)
QVQLKESGPGLVAPSQSLSITCTVSGFLLISNGVHWVRQPPGKGLEWLGVIWAGGNTNYN
SALMSRVSISKDNSKSQVFLKMKSLQTDDTAMYYCARDFYDYDVFYYAMDYWGQGTSVTV
SSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

Sequence of entity 3 (C), FASTA

>2VIR_3 HEMAGGLUTININ (chains C)
TITDDQIEVTDATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQDETWDLF
VERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGF
FSRLNWLTKSGSTYPVLDVTMPNNDNFDKLYIWGIHHPSTNQEQTSLYVQASGRVTVSTR
RSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSI
MRSDAPIDTCISECITPDGSIPNDKPFQNVNKITYGACPKYV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Antigen distortion allows influenza virus to escape neutralization. Fleury, D., Wharton, S.A., Skehel, J.J. et al. Nat Struct Biol (1998) 5:119-123. DOI 10.1038/nsb0298-119 · PubMed

Other PDB entries of the same protein (UniProt G0YP42 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NGP 2.4 Å, N1G9 (IgG1-lambda) FAB fragment complexed with (4-hydroxy-3-nitrophenyl) acetate
1NGQ 2.4 Å, N1G9 (IgG1-lambda) FAB fragment
1PG7 2.5 Å, Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab
1ETZ 2.6 Å, The three-dimensional structure of an anti-sweetener FAB, NC10.14, shows the extent of…
2OP4 2.85 Å, Crystal Structure of Quorum-Quenching Antibody 1G9
2NTF 3.18 Å, Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine…
2VIS 3.25 Å, Influenza virus hemagglutinin, (ESCAPE) mutant with thr 131 replaced by ile, complexed…
2VIT 3.25 Å, Influenza virus hemagglutinin, mutant with thr 155 replaced by ile, complexed with a…
3RHW 3.26 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab and ivermectin
3RIF 3.35 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and…
3RI5 3.4 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and…
3RIA 3.8 Å, C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and…

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