5XRT: Hemagglutinin

Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin. Determined by X-ray diffraction at 3.15 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2)), Influenza A virus
Chains: 8
Atoms: 16,943
Mol. weight: 246.79 kDa
Ligands: CAC, NAG
Released: 25 Jul 2018

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

Secondary structure: helices and β-sheets

5XRT contains 45 α-helices and 184 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: 7 helices, 37 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	50-54	5	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	136-142	7	11
β-strand	144-146	3	11
β-strand	151-153	3	9
β-strand	155-156	2	10
α-helix	162-163	2
β-strand	164-169	6	12
β-strand	176-184	9	9
α-helix	188-195	8
β-strand	202-205	4	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	242-247	6	12
β-strand	251-254	4	9
β-strand	256-259	4	9
β-strand	266-269	4	7
α-helix	272	1
β-strand	273-278	6	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
β-strand	321	1	3

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	15
β-strand	10	1	15
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	32-37	6	1
α-helix	38-55	18
α-helix	76-126	51
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-170	12

Chain C: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	16
β-strand	18	1	17
β-strand	24-26	3	18
β-strand	34-36	3	18
β-strand	39-41	3	19
β-strand	43-44	2	20
β-strand	50-54	5	21
β-strand	58-60	3	22
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	23
β-strand	86-89	4	22
β-strand	100-101	2	24
α-helix	105-115	11
β-strand	117	1	23
β-strand	120-122	3	24
β-strand	130-131	2	25
β-strand	136-140	5	26
β-strand	145-146	2	26
β-strand	151-153	3	24
β-strand	155-156	2	25
β-strand	164-169	6	27
β-strand	175-184	10	24
α-helix	188-195	8
β-strand	201-205	5	27
β-strand	210-213	4	27
α-helix	215-217	3
β-strand	223	1	28
β-strand	226	1	28
β-strand	229-237	9	24
β-strand	242-249	8	27
β-strand	251-254	4	24
β-strand	256-260	5	24
β-strand	266-269	4	22
β-strand	273-278	6	21
β-strand	281	1	29
β-strand	282	1	30
β-strand	288	1	29
β-strand	294-295	2	20
β-strand	302	1	30
β-strand	303-304	2	31
α-helix	306	1
β-strand	307-308	2	20
β-strand	315-317	3	19
β-strand	321	1	18

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	14	1	17
β-strand	22-27	6	16
β-strand	32-36	5	16
α-helix	38-55	18
β-strand	61-62	2	31
α-helix	76-125	50
β-strand	130-132	3	16
β-strand	137-140	4	16
α-helix	146-153	8
α-helix	160-170	11

Chain E: 5 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	32
β-strand	18	1	33
β-strand	24-26	3	34
β-strand	34-36	3	34
β-strand	39-41	3	35
β-strand	43-44	2	36
β-strand	50-52	3	37
β-strand	58-60	3	38
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	39
β-strand	86-89	4	38
β-strand	100-101	2	40
α-helix	105-115	11
β-strand	117	1	39
β-strand	120-122	3	40
β-strand	131	1	41
β-strand	136-141	6	42
β-strand	144-146	3	42
β-strand	151-153	3	40
β-strand	155	1	41
β-strand	164-169	6	43
β-strand	176-184	9	40
α-helix	188-195	8
β-strand	202-205	4	43
β-strand	210-213	4	43
β-strand	223	1	44
β-strand	226	1	44
β-strand	229-237	9	40
β-strand	242-247	6	43
β-strand	251-254	4	40
β-strand	256-259	4	40
β-strand	266-269	4	38
β-strand	273-275	3	37
β-strand	281-283	3	45
β-strand	286-288	3	45
β-strand	294-295	2	36
β-strand	302	1	45
β-strand	303-304	2	46
α-helix	306	1
β-strand	307-308	2	36
β-strand	315-317	3	35
β-strand	321	1	34

Chain F: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	47
β-strand	10	1	47
β-strand	14	1	33
β-strand	22-27	6	32
β-strand	32-36	5	32
α-helix	38-55	18
β-strand	61-62	2	46
α-helix	76-126	51
β-strand	130-132	3	32
β-strand	137-140	4	32
α-helix	146-152	7
α-helix	159-161	3
α-helix	163-170	8

Chain G: 7 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	48
β-strand	12-17	6	49
β-strand	18	1	50
α-helix	23	1
β-strand	24-26	3	51
β-strand	34-36	3	51
β-strand	39-41	3	52
β-strand	43-44	2	53
β-strand	50-52	3	54
β-strand	58-60	3	55
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	56
β-strand	86-89	4	55
β-strand	100-101	2	57
α-helix	105-115	11
β-strand	117	1	56
β-strand	120-122	3	57
β-strand	130-131	2	58
β-strand	136-140	5	59
β-strand	145-146	2	59
β-strand	151-153	3	57
β-strand	155-156	2	58
α-helix	162-163	2
β-strand	164-168	5	60
β-strand	177-184	8	57
α-helix	188-195	8
β-strand	202-205	4	60
β-strand	210-213	4	60
β-strand	223	1	61
β-strand	226	1	61
β-strand	229-236	8	57
β-strand	243-247	5	60
β-strand	251-254	4	57
β-strand	256-258	3	57
β-strand	266-269	4	55
β-strand	273-275	3	54
β-strand	281	1	62
β-strand	282	1	63
β-strand	288	1	62
β-strand	294-295	2	53
β-strand	302	1	63
β-strand	303-304	2	64
α-helix	306	1
β-strand	307-308	2	53
β-strand	315-317	3	52
β-strand	321	1	51

Chain H: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	65
β-strand	10	1	65
β-strand	14	1	50
β-strand	22-28	7	49
β-strand	31-37	7	49
α-helix	39-56	18
β-strand	61-62	2	64
α-helix	76-126	51
β-strand	130-132	3	48
β-strand	137	1	49
β-strand	138-140	3	48
α-helix	146-152	7
α-helix	159-162	4
α-helix	163-166	4
α-helix	167-169	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C, E, G	protein	329	Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))	I0AXC3
Hemagglutinin	B, D, F, H	protein	174	Influenza A virus	R9XUW5

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

>5XRT_1 Hemagglutinin (chains A, C, E, G)
QKLPGSDNSMATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGRICNSPHQILD
GKNCTLIDALLGDPHCDDFQNKEWDLFVERSTAYSNCYPYYVPDYATLRSLVASSGNLEF
TQESFNWTGVAQDGSSYACRRGSVNSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIW
GVHHPGTDKDQTNLYVQASGRVIVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPG
DILLINSTGNLIAPRGYFKIQSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKI
TYGACPRYVKQNTLKLATGMRNVPEKQTR

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

>5XRT_2 Hemagglutinin (chains B, D, F, H)
GIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQITGKLNRVIKKTN
EKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMSKLFE
RTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDIYRNEALNNRFQIK

Ligands and cofactors

ID	Name	Formula	Copies
CAC	Cacodylate ion	C2 H6 As O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA. Bangaru, S., Zhang, H., Gilchuk, I.M. et al. Nat Commun (2018) 9:2669-2669. DOI 10.1038/s41467-018-04704-9 · PubMed

Other PDB entries of the same protein (UniProt I0AXC3), best resolution first:

5XRS 2.91 Å, Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin in complex…
5W42 3.57 Å, Crystal structure of human monoclonal antibody H3v-47 in complex with influenza virus…

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