5XRS: Hemagglutinin

Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin in complex with LSTc. Determined by X-ray diffraction at 2.91 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))
Chains: 8
Atoms: 16,918
Mol. weight: 247.1 kDa
Ligands: CAC, NAG
Released: 25 Jul 2018

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

Secondary structure: helices and β-sheets

5XRS contains 49 α-helices and 177 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	12-17	6	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	131	1	10
β-strand	141	1	11
β-strand	144	1	11
β-strand	151-153	3	9
β-strand	155	1	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	302-304	3	14
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chain B: 5 helices, 8 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
β-strand	61-62	2	14
α-helix	76-126	51
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-152	7
α-helix	159-161	3
α-helix	163-170	8

Chain C: 8 helices, 37 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	50-52	3	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	131	1	25
β-strand	136-141	6	26
β-strand	144-146	3	26
β-strand	151-153	3	24
β-strand	155	1	25
α-helix	162-163	2
β-strand	164-169	6	27
β-strand	176-184	9	24
α-helix	188-195	8
α-helix	198	1
β-strand	202-205	4	27
β-strand	210-213	4	27
α-helix	220-222	3
β-strand	223	1	28
β-strand	226	1	28
β-strand	229-237	9	24
β-strand	242-247	6	27
β-strand	251-254	4	24
β-strand	256-259	4	24
β-strand	266-269	4	22
β-strand	273-275	3	21
β-strand	281-283	3	29
β-strand	286-288	3	29
β-strand	294-295	2	20
β-strand	302-304	3	29
α-helix	306	1
β-strand	307-308	2	20
β-strand	315-317	3	19
β-strand	321	1	18

Chain D: 6 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	29
α-helix	76-126	51
β-strand	130-132	3	16
β-strand	137-140	4	16
α-helix	146-152	7
α-helix	159-161	3
α-helix	163-170	8

Chain E: 6 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	30
β-strand	18	1	31
β-strand	24-26	3	32
β-strand	34-36	3	32
β-strand	39-41	3	33
β-strand	43-44	2	34
β-strand	50-52	3	35
β-strand	58-60	3	36
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	37
β-strand	86-89	4	36
β-strand	100-101	2	38
α-helix	105-115	11
β-strand	117	1	37
β-strand	120-122	3	38
β-strand	130-131	2	39
β-strand	136-141	6	40
β-strand	144-146	3	40
β-strand	151-153	3	38
β-strand	155-156	2	39
β-strand	164-169	6	41
β-strand	176-184	9	38
α-helix	188-195	8
β-strand	201-206	6	41
β-strand	209-213	5	41
α-helix	215-217	3
β-strand	223	1	42
β-strand	226	1	42
β-strand	229-237	9	38
β-strand	242-249	8	41
β-strand	251-254	4	38
β-strand	256-259	4	38
β-strand	266-269	4	36
β-strand	273-275	3	35
β-strand	281-282	2	43
β-strand	288	1	43
β-strand	294-295	2	34
β-strand	302-304	3	43
α-helix	306	1
β-strand	307-308	2	34
β-strand	315-317	3	33
β-strand	321	1	32

Chain F: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	44
β-strand	10	1	44
β-strand	14	1	31
β-strand	22-27	6	30
β-strand	34-37	4	30
α-helix	38-55	18
β-strand	61-62	2	43
α-helix	76-126	51
β-strand	130-132	3	30
β-strand	137-140	4	30
α-helix	146-153	8
α-helix	159-161	3
α-helix	163-170	8

Chain G: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	45
β-strand	18	1	46
β-strand	24-26	3	47
β-strand	34-36	3	47
β-strand	39-41	3	48
β-strand	43-44	2	49
β-strand	51-54	4	50
β-strand	58-60	3	51
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	52
β-strand	86-89	4	51
β-strand	100-101	2	53
α-helix	105-115	11
β-strand	117	1	52
β-strand	120-122	3	53
β-strand	130-131	2	54
β-strand	136-140	5	55
β-strand	145-146	2	55
β-strand	151-153	3	53
β-strand	155-156	2	54
α-helix	162-163	2
β-strand	164-169	6	56
β-strand	176-184	9	53
α-helix	188-195	8
β-strand	202-205	4	56
β-strand	210-213	4	56
β-strand	223	1	57
β-strand	226	1	57
β-strand	229-236	8	53
β-strand	242-247	6	56
β-strand	251-254	4	53
β-strand	256-259	4	53
α-helix	260	1
β-strand	266-269	4	51
β-strand	274-278	5	50
β-strand	281-283	3	58
β-strand	286-288	3	58
β-strand	294-295	2	49
β-strand	302	1	58
β-strand	303	1	59
α-helix	306	1
β-strand	307-308	2	49
β-strand	315-317	3	48
β-strand	321	1	47

Chain H: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	60
β-strand	10	1	60
β-strand	14	1	46
β-strand	24-27	4	45
α-helix	46-49	4
α-helix	51-54	4
β-strand	62	1	59
α-helix	76-111	36
β-strand	138-140	3	45
α-helix	150-153	4
α-helix	163-165	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 (A/swine/Minnesota/A01134337/2010(H3N2))	I0AXC3

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

>5XRS_1 Hemagglutinin (chains A, C, E, G)
QKLPGSDNSMATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGRICNSPHQILD
GKNCTLIDALLGDPHCDDFQNKEWDLFVERSTAYSNCYPYYVPDYATLRSLVASSGNLEF
TQESFNWTGVAQDGSSYACRRGSVNSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIW
GVHHPGTDKDQTNLYVQASGRVIVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPG
DILLINSTGNLIAPRGYFKIQSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKI
TYGACPRYVKQNTLKLATGMRNVPEKQTR

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

>5XRS_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:

5XRT 3.15 Å, Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin
5W42 3.57 Å, Crystal structure of human monoclonal antibody H3v-47 in complex with influenza virus…

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