5UGY: Influenza hemagglutinin

Influenza hemagglutinin in complex with a neutralizing antibody. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Jan 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Homo sapiens
Chains: 12
Atoms: 21,882
Mol. weight: 313.21 kDa
Ligands: NAG
Released: 25 Jan 2017

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

Secondary structure: helices and β-sheets

5UGY contains 58 α-helices and 288 β-strands across 12 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: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	12	1	2
β-strand	19-20	2	3
β-strand	28-29	2	3
β-strand	30	1	4
β-strand	33-35	3	5
β-strand	37-38	2	6
β-strand	45-48	4	7
β-strand	51	1	7
α-helix	52-53	2
β-strand	54-55	2	8
β-strand	59	1	9
α-helix	61-66	6
β-strand	80	1	10
β-strand	83-85	3	8
β-strand	91	1	9
β-strand	99	1	11
α-helix	102-108	7
β-strand	112	1	10
β-strand	114-119	6	11
β-strand	131	1	12
β-strand	136-140	5	13
β-strand	145-146	2	13
β-strand	151-153	3	11
β-strand	155	1	12
β-strand	164-169	6	14
β-strand	175-184	10	11
α-helix	188-195	8
β-strand	202-206	5	14
β-strand	209-213	5	14
β-strand	229-237	9	11
β-strand	242-247	6	14
β-strand	251-254	4	11
β-strand	256-261	6	11
β-strand	268-270	3	8
α-helix	273-274	2
β-strand	275-280	6	7
β-strand	282-283	2	15
β-strand	289	1	15
β-strand	295-296	2	6
β-strand	303-305	3	15
α-helix	307	1
β-strand	308-309	2	6
β-strand	316-318	3	5
β-strand	322	1	4

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	506	1	16
β-strand	510	1	16
β-strand	514	1	2
β-strand	522-526	5	1
β-strand	528	1	17
β-strand	531	1	17
β-strand	534-536	3	1
α-helix	538-556	19
β-strand	563-565	3	15
α-helix	575-623	49
β-strand	630-633	4	1
β-strand	637-640	4	1
α-helix	646-653	8
α-helix	663-672	10

Chain C: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	18
β-strand	12	1	19
β-strand	19-20	2	20
β-strand	28-29	2	20
β-strand	30	1	21
β-strand	33-35	3	22
β-strand	37-38	2	23
β-strand	45-48	4	24
β-strand	51	1	24
α-helix	52-53	2
β-strand	54-55	2	25
β-strand	59	1	26
α-helix	61-66	6
β-strand	80	1	27
β-strand	83-85	3	25
β-strand	91	1	26
β-strand	99	1	28
α-helix	102-108	7
β-strand	112	1	27
β-strand	114-119	6	28
β-strand	130-131	2	29
β-strand	136-140	5	30
β-strand	145-146	2	30
β-strand	151-153	3	28
β-strand	155-156	2	29
β-strand	164-169	6	31
β-strand	175-184	10	28
α-helix	188-195	8
β-strand	202-206	5	31
β-strand	209-213	5	31
β-strand	229-237	9	28
β-strand	242-247	6	31
β-strand	251-254	4	28
β-strand	256-261	6	28
β-strand	268-270	3	25
α-helix	273-274	2
β-strand	275-280	6	24
β-strand	282-283	2	32
β-strand	289	1	32
β-strand	295-296	2	23
β-strand	303-304	2	32
α-helix	307	1
β-strand	308-309	2	23
β-strand	316-318	3	22
β-strand	322	1	21

Chains D and F: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	506	1	33
β-strand	510	1	33
β-strand	514	1	19
β-strand	522-526	5	18
β-strand	528	1	34
β-strand	531	1	34
β-strand	534-536	3	18
α-helix	538-556	19
β-strand	564-565	2	32
α-helix	575-623	49
β-strand	630-633	4	18
β-strand	637-640	4	18
α-helix	646-653	8
α-helix	663-672	10

Chain E: 7 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	35
β-strand	12	1	36
β-strand	19-20	2	37
β-strand	28-29	2	37
β-strand	30	1	38
β-strand	33-35	3	39
β-strand	37-38	2	40
β-strand	45-48	4	41
β-strand	51	1	41
α-helix	52-53	2
β-strand	54-55	2	42
β-strand	59	1	43
α-helix	61-66	6
β-strand	80	1	44
β-strand	83-85	3	42
β-strand	91	1	43
β-strand	99	1	45
α-helix	102-108	7
β-strand	112	1	44
β-strand	114-119	6	45
β-strand	131	1	46
β-strand	136-140	5	47
β-strand	145-146	2	47
β-strand	151	1	48
β-strand	155	1	46
β-strand	164-169	6	49
β-strand	175-184	10	45
α-helix	188-195	8
β-strand	202-206	5	49
β-strand	209-213	5	49
α-helix	215-217	3
β-strand	229-237	9	45
β-strand	242-247	6	49
β-strand	251-252	2	45
β-strand	254	1	48
β-strand	256-261	6	45
β-strand	268-270	3	42
α-helix	273-274	2
β-strand	275-280	6	41
β-strand	282-283	2	50
β-strand	289	1	50
β-strand	295-296	2	40
β-strand	303-304	2	50
α-helix	307	1
β-strand	308-309	2	40
β-strand	316-318	3	39
β-strand	322	1	38

Chains H and J: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	53
β-strand	10-12	3	54
β-strand	18-25	8	53
β-strand	33-39	7	54
β-strand	45-51	7	54
β-strand	58-60	3	54
β-strand	68-72	5	53
β-strand	78-83	6	53
α-helix	88-90	3
β-strand	92-99	8	54
β-strand	101	1	55
β-strand	112	1	55
β-strand	116	1	54
β-strand	120-124	5	54
β-strand	130	1	56
α-helix	131-132	2
β-strand	133-137	5	57
β-strand	148-158	11	57
β-strand	159	1	56
β-strand	164-167	4	58
α-helix	168-170	3
β-strand	172	1	58
β-strand	176-178	3	57
α-helix	179-181	3
β-strand	182-183	2	57
β-strand	189-198	10	57
β-strand	202	1	59
β-strand	205	1	59
β-strand	208-213	6	58
β-strand	218-223	6	58

Chain I: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	60
β-strand	10-12	3	61
β-strand	18-25	8	60
β-strand	33-39	7	61
β-strand	45-51	7	61
β-strand	58-60	3	61
β-strand	68-72	5	60
β-strand	78-83	6	60
α-helix	88-90	3
β-strand	92-99	8	61
β-strand	101	1	62
β-strand	112	1	62
β-strand	116	1	61
β-strand	120-124	5	61
β-strand	130	1	63
α-helix	131-132	2
β-strand	133-137	5	64
β-strand	148-149	2	65
β-strand	152-158	7	64
β-strand	159	1	63
β-strand	164-167	4	66
α-helix	168-170	3
β-strand	172	1	66
β-strand	176-178	3	64
α-helix	179-181	3
β-strand	182-183	2	64
β-strand	189-195	7	64
β-strand	197-198	2	65
β-strand	202	1	67
β-strand	205	1	67
β-strand	208-213	6	66
β-strand	218-223	6	66

Chains L, M and N: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	75
β-strand	9-12	4	76
β-strand	18-23	6	75
α-helix	27-29	3
β-strand	33-37	5	76
β-strand	44-48	5	76
β-strand	52	1	76
β-strand	61-66	6	75
β-strand	69-74	6	75
β-strand	83-91	9	76
β-strand	96-99	4	76
β-strand	103-107	5	76
α-helix	114-115	2
β-strand	116-120	5	77
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	77
β-strand	147-152	6	78
β-strand	155-157	3	78
β-strand	161-163	3	77
β-strand	167-168	2	77
β-strand	174-182	9	77
α-helix	184-188	5
β-strand	193-199	7	78
β-strand	202-208	7	78

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A, C, E	protein	323	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8A6
Hemagglutinin HA2	B, D, F	protein	173	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8I1
CH65 heavy chain	H, I, J	protein	227	Homo sapiens	S6C4S0 (AlphaFold model)
CH65 light chain	L, M, N	protein	210	Homo sapiens	Q8N355 (AlphaFold model)

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

>5UGY_1 Hemagglutinin HA1 (chains A, C, E)
EDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAG
WILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPK
ESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVH
HPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTLLEPGDTI
IFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTI
GECPKYVRSAKLRMVTGLRNIPS

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

>5UGY_2 Hemagglutinin HA2 (chains B, D, F)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKI

Sequence of entity 3 (H, I, J), FASTA

>5UGY_3 CH65 heavy chain (chains H, I, J)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTDYHINWVRQAPGQGLEWMGWIHPNSGDTNY
AQKFQGWVTMTRDTAISTAYMEVNGLKSDDTAVYYCARGGLEPRSVDYYYYGMDVWGQGT
TVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 4 (L, M, N), FASTA

>5UGY_4 CH65 light chain (chains L, M, N)
SVLTQPPSVSVAPGQTARITCGGNDIGRKSVHWNQQKPGQAPVLVVCYDSDRPSGIPERF
SGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHVIFGGGTKLTVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHRSYSCQVTHEGSTVEKTVAPT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Broadly neutralizing human antibody that recognizes the receptor-binding pocket of influenza virus hemagglutinin. Whittle, J.R., Zhang, R., Khurana, S. et al. Proc Natl Acad Sci U S A (2011) 108:14216-14221. DOI 10.1073/pnas.1111497108 · PubMed

Other PDB entries of the same protein (UniProt A7Y8A6), best resolution first:

7JIX 3.9 Å, Murine antibody that engages the influenza hemagglutinin receptor binding site

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