5W08: A/Texas/50/2012(H3N2) Influenza hemagglutinin

A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab. Determined by X-ray diffraction at 2.6 Å resolution. Released 14 Feb 2018.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Influenza A virus (A/Texas/50/2012(H3N2)), Homo sapiens
Chains: 18
Atoms: 34,382
Mol. weight: 498.03 kDa
Ligands: NAG
Released: 14 Feb 2018

Explore 5W08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W08 contains 113 α-helices and 465 β-strands across 18 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.

Chains A and F: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	43-44	2	1
β-strand	51-52	2	2
β-strand	58-60	3	3
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	4
β-strand	86-89	4	3
β-strand	100-101	2	5
α-helix	105-113	9
β-strand	117	1	4
β-strand	120-122	3	5
β-strand	130-131	2	6
β-strand	135	1	7
β-strand	136-141	6	8
β-strand	144-146	3	8
β-strand	151-153	3	5
β-strand	155-156	2	6
β-strand	164-169	6	9
β-strand	175-184	10	5
α-helix	188-195	8
β-strand	202-205	4	9
β-strand	210-213	4	9
β-strand	229-237	9	5
β-strand	242-247	6	9
β-strand	251-254	4	5
β-strand	256-260	5	5
β-strand	266-269	4	3
α-helix	272-273	2
β-strand	274-275	2	2
β-strand	281-283	3	10
β-strand	286-287	2	10
β-strand	294-295	2	1
β-strand	302-303	2	10
α-helix	306	1
β-strand	307-308	2	1

Chain B: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	43-44	2	11
β-strand	51-52	2	12
β-strand	58-60	3	13
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	14
β-strand	86-89	4	13
β-strand	100-101	2	15
α-helix	105-113	9
β-strand	117	1	14
β-strand	120-122	3	15
β-strand	130-131	2	16
β-strand	135	1	17
β-strand	136-140	5	18
β-strand	145-146	2	18
β-strand	151-153	3	15
β-strand	155-156	2	16
β-strand	164-169	6	19
β-strand	176-184	9	15
α-helix	188-195	8
β-strand	202-205	4	19
β-strand	210-213	4	19
β-strand	229-237	9	15
β-strand	242-247	6	19
β-strand	251-254	4	15
β-strand	256-259	4	15
α-helix	260	1
β-strand	266-269	4	13
α-helix	272-273	2
β-strand	274-275	2	12
β-strand	281-283	3	20
β-strand	286-287	2	20
β-strand	294-295	2	11
β-strand	302-303	2	20
α-helix	306	1
β-strand	307-308	2	11

Chains C and E: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	43-44	2	21
β-strand	51-52	2	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	105-113	9
β-strand	117	1	24
β-strand	120-122	3	25
β-strand	130-131	2	26
β-strand	135	1	27
β-strand	136-141	6	28
β-strand	144-146	3	28
β-strand	151-153	3	25
β-strand	155-156	2	26
β-strand	164-169	6	29
β-strand	176-184	9	25
α-helix	188-195	8
β-strand	202-205	4	29
β-strand	210-213	4	29
β-strand	229-237	9	25
β-strand	242-247	6	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	274-275	2	22
β-strand	281-283	3	30
β-strand	286-287	2	30
β-strand	294-295	2	21
β-strand	302-303	2	30
α-helix	306	1
β-strand	307-308	2	21

Chain D: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	43-44	2	31
β-strand	51-52	2	32
β-strand	58-60	3	33
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	34
β-strand	86-89	4	33
β-strand	100-101	2	35
α-helix	105-113	9
β-strand	117	1	34
β-strand	120-122	3	35
β-strand	131	1	36
β-strand	135	1	37
β-strand	136-141	6	38
β-strand	144-146	3	38
β-strand	151-153	3	35
β-strand	155	1	36
β-strand	164-169	6	39
β-strand	175-184	10	35
α-helix	188-195	8
β-strand	202-205	4	39
β-strand	210-213	4	39
β-strand	229-237	9	35
β-strand	242-247	6	39
β-strand	251-254	4	35
β-strand	256-260	5	35
β-strand	266-269	4	33
α-helix	272-273	2
β-strand	274-275	2	32
β-strand	281-283	3	40
β-strand	286-287	2	40
β-strand	294-295	2	31
β-strand	302-303	2	40
α-helix	306	1
β-strand	307-308	2	31

Chains G and I: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	61
β-strand	10-12	3	62
β-strand	18-25	8	61
α-helix	29-31	3
β-strand	32-39	8	62
β-strand	45-51	7	62
β-strand	58-60	3	62
β-strand	68-73	6	61
β-strand	78-83	6	61
α-helix	88-90	3
β-strand	92-102	11	62
β-strand	104-105	2	7
β-strand	110-111	2	7
β-strand	120-123	4	62
β-strand	127-131	5	62
β-strand	137	1	63
α-helix	138-139	2
β-strand	140-144	5	64
α-helix	145-147	3
β-strand	155-165	11	64
β-strand	166	1	63
β-strand	171-174	4	65
α-helix	175-177	3
β-strand	179	1	65
β-strand	183-185	3	64
α-helix	186-188	3
β-strand	189-190	2	64
β-strand	196-205	10	64
α-helix	206-208	3
β-strand	214-220	7	65
β-strand	225-231	7	65

Chains H and P: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	66
β-strand	5	1	67
β-strand	9-12	4	68
β-strand	18-23	6	67
β-strand	36-40	5	68
β-strand	47-50	4	68
β-strand	51	1	69
β-strand	55	1	69
β-strand	64-68	5	67
β-strand	72-77	6	67
α-helix	82-84	3
β-strand	86-93	8	68
β-strand	97-99	3	68
β-strand	100	1	66
β-strand	103-107	5	68
β-strand	113	1	70
α-helix	114-115	2
β-strand	116-120	5	71
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	71
β-strand	142	1	70
β-strand	147-152	6	72
β-strand	155-157	3	72
β-strand	161-163	3	71
α-helix	164-166	3
β-strand	167-168	2	71
β-strand	174-182	9	71
α-helix	184-189	6
β-strand	193-199	7	72
β-strand	202-208	7	72

Chain J: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	78
β-strand	5	1	79
β-strand	9-12	4	80
β-strand	18-23	6	79
β-strand	36-40	5	80
β-strand	47-50	4	80
β-strand	51	1	81
β-strand	55	1	81
β-strand	64-69	6	79
β-strand	72-77	6	79
α-helix	82-84	3
β-strand	87-93	7	80
β-strand	97-99	3	80
β-strand	100	1	78
β-strand	103-107	5	80
β-strand	113	1	82
α-helix	114-115	2
β-strand	116-120	5	83
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	83
β-strand	142	1	82
β-strand	147-152	6	84
β-strand	155-157	3	84
β-strand	161-163	3	83
α-helix	164-166	3
β-strand	167-168	2	83
β-strand	174-182	9	83
α-helix	184-189	6
β-strand	193-199	7	84
β-strand	202-208	7	84

Chain K: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	85
β-strand	10-12	3	86
β-strand	18-25	8	85
α-helix	29-31	3
β-strand	32-39	8	86
β-strand	45-51	7	86
β-strand	58-60	3	86
β-strand	65	1	85
β-strand	68-73	6	85
β-strand	78-83	6	85
α-helix	88-90	3
β-strand	92-102	11	86
β-strand	104-105	2	27
β-strand	110-111	2	27
β-strand	120-123	4	86
β-strand	127-131	5	86
β-strand	137	1	87
α-helix	138-139	2
β-strand	140-144	5	88
α-helix	145-147	3
β-strand	155-165	11	88
β-strand	166	1	87
β-strand	171-174	4	89
α-helix	175-177	3
β-strand	179	1	89
β-strand	183-185	3	88
α-helix	186-188	3
β-strand	189-190	2	88
β-strand	196-205	10	88
α-helix	206-210	5
β-strand	215-220	6	89
β-strand	225-230	6	89

6 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
Hemagglutinin HA1	A, B, C, D, E, F	protein	291	Influenza A virus (A/Texas/50/2012(H3N2))	R4L1D1
K03.12 antibody heavy chain	G, I, K, M, O, Q	protein	244	Homo sapiens	S6C4S0 (AlphaFold model)
K03.12 antibody light chain	H, J, L, N, P, R	protein	214	Homo sapiens	Q6IPQ0 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5W08_1 Hemagglutinin HA1 (chains A, B, C, D, E, F)
TNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSN
CYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTH
LNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPN
IGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGK
CKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGGALEVLFQ

Sequence of entity 2 (G, I, K, M, O, Q), FASTA

>5W08_2 K03.12 antibody heavy chain (chains G, I, K, M, O, Q)
EVQLVQSGAEVKKPGASVKVSCKTSGYTFTAYYLHWVRQAPGQGFEWMAWINPNTGDTNY
AQKFQGRVTLSRDTSITTAYMELTRLRSDDTAVYYCAKDLTLMYVFDSGWARGAHDYYGM
DVWGQGTTVAVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALT
SGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHH
HHHH

Sequence of entity 3 (H, J, L, N, P, R), FASTA

>5W08_3 K03.12 antibody light chain (chains H, J, L, N, P, R)
PSALTQPASVSGSPGQSVTISCTGTNSDVGTFDLVSWYQQYPGKAPKLIIYEGSRRPSGV
SDRFSGSKSGNTASLTISGLQAEDEADYYCSSYAGSVVFGGGTKLTVLGQPKGAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16

Water and common crystallization additives (GOL) are not listed.

Primary citation

Memory B Cells that Cross-React with Group 1 and Group 2 Influenza A Viruses Are Abundant in Adult Human Repertoires. McCarthy, K.R., Watanabe, A., Kuraoka, M. et al. Immunity (2018) 48:174-184.e9. DOI 10.1016/j.immuni.2017.12.009 · PubMed

Other PDB entries of the same protein (UniProt R4L1D1), best resolution first:

6E4X 2.25 Å, Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)
6XQ2 3.0 Å, Human antibody S8V2-37 in complex with the influenza hemagglutinin head domain of…
6XPY 3.6 Å, Human antibody S1V2-58 in complex with the influenza hemagglutinin head domain of…
6XPR 4.09 Å, Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain…
6XPQ 4.2 Å, Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of…

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