6BKM: Hemagglutinin

Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D mutant apo form. Determined by X-ray diffraction at 2.2 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Influenza A virus (strain A/Hong Kong/1/1968 H3N2), Influenza A virus (strain A/Northern Territory/60/1968 H3N2)
Chains: 6
Atoms: 12,550
Mol. weight: 171.61 kDa
Ligands: TAM, NAG
Released: 28 Feb 2018

Explore 6BKM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BKM contains 37 α-helices and 141 β-strands across 6 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: 9 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	18	1	2
β-strand	24-26	3	3
β-strand	34-36	3	3
β-strand	39-41	3	4
β-strand	43-44	2	5
β-strand	51-54	4	6
β-strand	58-60	3	7
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	8
β-strand	86-89	4	7
β-strand	100-101	2	9
α-helix	105-115	11
β-strand	117	1	8
β-strand	120-122	3	9
β-strand	130-131	2	10
β-strand	136-141	6	11
β-strand	144-146	3	11
β-strand	151-153	3	9
β-strand	155-156	2	10
β-strand	157	1	12
β-strand	160	1	12
α-helix	162-163	2
β-strand	164-169	6	13
β-strand	176-184	9	9
α-helix	188-195	8
β-strand	201-205	5	13
β-strand	210-213	4	13
β-strand	223	1	14
β-strand	226	1	14
β-strand	229-237	9	9
β-strand	242-249	8	13
β-strand	251-254	4	9
β-strand	256-259	4	9
α-helix	260	1
β-strand	266-269	4	7
α-helix	272-273	2
β-strand	274-278	5	6
β-strand	281-283	3	15
β-strand	286-288	3	15
β-strand	294-295	2	5
β-strand	302-304	3	15
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3
α-helix	324-326	3

Chains B, D and F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	16
β-strand	10	1	16
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-55	18
β-strand	61-62	2	15
α-helix	76-125	50
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-170	12

Chains C and E: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	17
β-strand	18	1	18
β-strand	24-26	3	19
β-strand	34-36	3	19
β-strand	39-41	3	20
β-strand	43-44	2	21
β-strand	51-54	4	22
β-strand	58-60	3	23
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	24
β-strand	86-89	4	23
β-strand	100-101	2	25
α-helix	105-115	11
β-strand	117	1	24
β-strand	120-122	3	25
β-strand	130-131	2	26
β-strand	136-141	6	27
β-strand	144-146	3	27
β-strand	151-153	3	25
β-strand	155-156	2	26
β-strand	157	1	28
β-strand	160	1	28
α-helix	162-163	2
β-strand	164-169	6	29
β-strand	176-184	9	25
α-helix	188-195	8
β-strand	201-205	5	29
β-strand	210-213	4	29
β-strand	223	1	30
β-strand	226	1	30
β-strand	229-237	9	25
β-strand	242-249	8	29
β-strand	251-254	4	25
β-strand	256-259	4	25
α-helix	260	1
β-strand	266-269	4	23
α-helix	272-273	2
β-strand	274-278	5	22
β-strand	281-283	3	31
β-strand	286-288	3	31
β-strand	294-295	2	21
β-strand	302-304	3	31
α-helix	306	1
β-strand	307-308	2	21
β-strand	315-317	3	20
β-strand	321	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C, E	protein	323	Influenza A virus (strain A/Hong Kong/1/1968 H3N2)	Q91MA7
Hemagglutinin	B, D, F	protein	174	Influenza A virus (strain A/Northern Territory/60/1968 H3N2)	P03436

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

>6BKM_1 Hemagglutinin (chains A, C, E)
ADPGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTL
IDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFT
WTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPS
TNQDQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVIN
SNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACP
KYVKQNTLKLATGMRNVPEKQTR

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

>6BKM_2 Hemagglutinin (chains B, D, F)
GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTN
EKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFE
KTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIK

Ligands and cofactors

ID	Name	Formula	Copies
TAM	Tris(hydroxyethyl)aminomethane	C7 H17 N O3	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site. Wu, N.C., Thompson, A.J., Xie, J. et al. Nat Commun (2018) 9:1264-1264. DOI 10.1038/s41467-018-03663-5 · PubMed

Other PDB entries of the same protein (UniProt Q91MA7), best resolution first:

4FNK 1.9 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin
8IB1 1.95 Å, Structure of the LAH31 Fab bound to an influenza virus HA epitope peptide
5UMN 1.97 Å, Crystal structure of C05 VPGSGW mutant bound to H3 influenza hemagglutinin, HA1 subunit
6NHR 2.1 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2…
6OCB 2.1 Å, Crystal structure of FluA-20 Fab in complex with the head domain of H3 (A/Hong…
5VTZ 2.15 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
7QA4 2.19 Å, Crystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglutinin at 2.2 Angstrom
6TZB 2.24 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in…
5VTV 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
5VU4 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
6BKQ 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D…
6NHP 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2…

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