6NZ7: Hemagglutinin HA1 chain

Crystal structure of broadly neutralizing Influenza A antibody 429 B01 in complex with Hemagglutinin Hong Kong 1968. Determined by X-ray diffraction at 2.95 Å resolution. Released 8 May 2019.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Influenza A virus (strain A/Hong Kong/1/1968 H3N2), Homo sapiens
Chains: 8
Atoms: 14,298
Mol. weight: 207.65 kDa
Ligands: NAG
Released: 8 May 2019

Explore 6NZ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NZ7 contains 59 α-helices and 180 β-strands across 8 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: 10 helices, 38 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
α-helix	90	1
β-strand	100-101	2	9
α-helix	105-115	11
β-strand	117	1	8
β-strand	120-122	3	9
β-strand	130-134	5	9
β-strand	136	1	10
α-helix	137-139	3
β-strand	146	1	10
β-strand	151-156	6	9
β-strand	157	1	11
β-strand	160	1	11
β-strand	164-169	6	12
β-strand	176-184	9	9
α-helix	188-195	8
β-strand	201-205	5	12
β-strand	210-213	4	12
β-strand	223	1	13
β-strand	226	1	13
β-strand	229-237	9	9
β-strand	242-249	8	12
β-strand	251-254	4	9
β-strand	256-259	4	9
β-strand	266-269	4	7
α-helix	272-273	2
β-strand	274-278	5	6
β-strand	281-283	3	14
β-strand	286-288	3	14
β-strand	294-295	2	5
β-strand	302	1	14
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
α-helix	320	1
β-strand	321	1	3
α-helix	322	1

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-73	36
α-helix	82-126	45
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-172	14

Chain E: 9 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	28
β-strand	18	1	29
β-strand	24-26	3	30
β-strand	34-36	3	30
β-strand	39-41	3	31
β-strand	43-44	2	32
β-strand	51-54	4	33
β-strand	58-60	3	34
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	35
β-strand	86-89	4	34
β-strand	101	1	36
α-helix	105-115	11
β-strand	117	1	35
β-strand	120-122	3	36
β-strand	131	1	37
β-strand	136	1	38
α-helix	137-139	3
β-strand	146	1	38
β-strand	151-153	3	36
β-strand	155	1	37
β-strand	157	1	39
β-strand	160	1	39
β-strand	164-169	6	40
β-strand	176-184	9	36
α-helix	188-195	8
β-strand	201-205	5	40
β-strand	210-213	4	40
β-strand	223	1	41
β-strand	226	1	41
β-strand	229-237	9	36
β-strand	242-249	8	40
β-strand	251-254	4	36
β-strand	256-259	4	36
β-strand	266-269	4	34
α-helix	272-273	2
β-strand	274-278	5	33
β-strand	281-283	3	42
β-strand	286-288	3	42
β-strand	294-295	2	32
β-strand	302	1	42
α-helix	306	1
β-strand	307-308	2	32
β-strand	315-317	3	31
α-helix	320	1
β-strand	321	1	30
α-helix	322	1

Chain F: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	29
β-strand	22-28	7	28
β-strand	31-36	6	28
α-helix	38-72	35
α-helix	82-126	45
β-strand	130-132	3	28
β-strand	137-140	4	28
α-helix	146-153	8
α-helix	159-162	4

Chain G: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	43
β-strand	10-12	3	44
β-strand	18-25	8	43
α-helix	29-31	3
β-strand	34-39	6	44
β-strand	45-51	7	44
β-strand	58-60	3	44
α-helix	62-64	3
β-strand	71-73	3	43
β-strand	78-83	6	43
α-helix	88-90	3
β-strand	92-99	8	44
α-helix	100-101	2
β-strand	102	1	45
β-strand	105	1	45
β-strand	112-115	4	44
β-strand	119-123	5	44
α-helix	127-128	2
β-strand	129	1	46
α-helix	130-131	2
β-strand	132-136	5	47
β-strand	148-157	10	47
β-strand	158	1	46
β-strand	163-166	4	48
α-helix	167-169	3
β-strand	171	1	48
β-strand	175-177	3	47
α-helix	178-180	3
β-strand	181-182	2	47
β-strand	188-196	9	47
β-strand	207-212	6	48
α-helix	213-215	3
β-strand	217-222	6	48

Chain H: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-12	3	16
β-strand	20-25	6	15
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	58-60	3	16
α-helix	62-64	3
β-strand	71-73	3	15
β-strand	78-81	4	15
β-strand	92-98	7	16
β-strand	99	1	17
α-helix	100-101	2
β-strand	102	1	18
β-strand	105	1	18
β-strand	112	1	17
β-strand	119-123	5	16
β-strand	129	1	19
α-helix	130-131	2
β-strand	132-136	5	20
β-strand	147-155	9	20
β-strand	157	1	21
β-strand	158	1	19
β-strand	163-166	4	22
α-helix	167-169	3
β-strand	171	1	22
β-strand	175-177	3	20
α-helix	178-180	3
β-strand	181-182	2	21
β-strand	188-189	2	21
β-strand	192-197	6	20
β-strand	207-212	6	22
α-helix	213-215	3
β-strand	217-222	6	22

Chain I: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	49
β-strand	10-14	5	50
β-strand	19-24	6	49
β-strand	33-38	6	50
α-helix	43-44	2
β-strand	45-49	5	50
β-strand	53-54	2	50
α-helix	55	1
β-strand	62-64	3	49
β-strand	70-75	6	49
α-helix	80-82	3
β-strand	84-90	7	50
β-strand	98	1	50
β-strand	102-107	6	50
β-strand	111	1	51
α-helix	112-113	2
β-strand	114-118	5	52
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	52
β-strand	140	1	51
β-strand	145-150	6	53
β-strand	153-155	3	53
β-strand	159-163	5	52
α-helix	164-167	4
β-strand	173-182	10	52
α-helix	183-186	4
β-strand	191-197	7	53
β-strand	205-210	6	53

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	23
β-strand	10-14	5	24
β-strand	18-23	6	23
β-strand	33-38	6	24
α-helix	43-44	2
β-strand	45-49	5	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-64	3	23
β-strand	71-76	6	23
α-helix	80-82	3
β-strand	84-90	7	24
β-strand	98	1	24
β-strand	102-107	6	24
β-strand	111	1	25
α-helix	112-113	2
β-strand	114-118	5	26
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	26
β-strand	140	1	25
β-strand	145-150	6	27
β-strand	153	1	27
β-strand	159-164	6	26
α-helix	165-167	3
β-strand	173-182	10	26
α-helix	183-187	5
β-strand	191-197	7	27
β-strand	205-210	6	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A, E	protein	319	Influenza A virus (strain A/Hong Kong/1/1968 H3N2)	Q91MA7
Hemagglutinin HA2 chain	B, F	protein	173	Influenza A virus (strain A/Hong Kong/1/1968 H3N2)	Q91MA7
429 B01 FAB heavy chain	G, H	protein	228	Homo sapiens	A8K008 (AlphaFold model)
429 B01 FAB light chain	I, L	protein	214	Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6NZ7_1 Hemagglutinin HA1 chain (chains A, E)
NSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLI
DALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTW
TGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPST
NQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSSRISIYWTIVKPGDVLVINS
NGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPK
YVKQNTLKLATGMRNVPEK

Sequence of entity 2 (B, F), FASTA

>6NZ7_2 Hemagglutinin HA2 chain (chains B, F)
GAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKF
HQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTR
RQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGV

Sequence of entity 3 (G, H), FASTA

>6NZ7_3 429 B01 FAB heavy chain (chains G, H)
QVQLVESGGGVVQPGRSLRLSCAASGFSFSTSVIHWVRQTPGKGLEWLAVISYDGSNKYY
ADSVQGRFTISRDNSNNTLYLQVNSLRPEDTAVYYCARGITVFGLLIINSAMDVWGQGTT
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 4 (I, L), FASTA

>6NZ7_4 429 B01 FAB light chain (chains I, L)
DIQMTQSPSSLSASVGDRVTITCRASQGISYNLAWYQQKPGRVPNLLIHAASRLQSGAPF
RFSGSGSGTDFTLTISSLQPEDVATYYCQKYDSVPLTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

Primary citation

Prolonged evolution of the memory B cell response induced by a replicating adenovirus-influenza H5 vaccine. Matsuda, K., Huang, J., Zhou, T. et al. Sci Immunol (2019) 4. DOI 10.1126/sciimmunol.aau2710 · 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
6BKM 2.2 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D…
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…

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