5W0D: Hemagglutinin HA1

Inferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006. Determined by X-ray diffraction at 1.9 Å resolution. Released 14 Feb 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Homo sapiens
Chains: 3
Atoms: 5,350
Mol. weight: 76.03 kDa
Released: 14 Feb 2018

Explore 5W0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W0D contains 23 α-helices and 74 β-strands across 3 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, 26 β-strands

Element	Residues	Length	Sheet
α-helix	52-53	2
β-strand	54-55	2	1
β-strand	59	1	2
α-helix	61-66	6
β-strand	80	1	3
β-strand	83-84	2	1
β-strand	91	1	2
β-strand	99	1	4
α-helix	102-108	7
β-strand	112	1	3
β-strand	114-119	6	4
α-helix	123-126	4
β-strand	131	1	5
β-strand	135	1	6
β-strand	136-141	6	7
β-strand	144-146	3	7
β-strand	151-153	3	4
β-strand	155	1	5
β-strand	157	1	8
β-strand	160	1	8
β-strand	164-169	6	9
β-strand	175-184	10	4
α-helix	188-195	8
β-strand	202-206	5	9
β-strand	209-213	5	9
α-helix	220-222	3
β-strand	223	1	10
β-strand	226	1	10
β-strand	229-237	9	4
β-strand	242-247	6	9
β-strand	251-254	4	4
β-strand	256-261	6	4

Chain B: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	46-51	6	12
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	104-105	2	6
α-helix	106-108	3
β-strand	110-111	2	6
β-strand	120-123	4	12
β-strand	127-131	5	12
α-helix	134-136	3
β-strand	137	1	13
α-helix	138-139	2
β-strand	140-144	5	14
β-strand	151	1	14
β-strand	155-165	11	14
β-strand	166	1	13
β-strand	171-174	4	15
α-helix	175-177	3
β-strand	179	1	15
β-strand	183-185	3	14
α-helix	186-188	3
β-strand	189-190	2	14
β-strand	196-205	10	14
α-helix	206-208	3
β-strand	215-220	6	15
α-helix	221-223	3
β-strand	225-230	6	15

Chain C: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	16
β-strand	9-12	4	17
β-strand	18-23	6	16
β-strand	36-40	5	17
β-strand	47-50	4	17
β-strand	51	1	18
β-strand	55	1	18
β-strand	64-69	6	16
β-strand	72-77	6	16
α-helix	82-84	3
β-strand	86-93	8	17
β-strand	97-99	3	17
β-strand	103-107	5	17
β-strand	113	1	19
α-helix	114-115	2
β-strand	116-120	5	20
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	20
β-strand	142	1	19
β-strand	147-152	6	21
β-strand	155-156	2	21
β-strand	161-163	3	20
α-helix	164-166	3
β-strand	167-168	2	20
β-strand	174-182	9	20
α-helix	184-188	5
β-strand	193-199	7	21
β-strand	202-208	7	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A	protein	223	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7UPX0
Lineage K03.12 UCA antibody heavy chain	B	protein	244	Homo sapiens	S6B2A6 (AlphaFold model)
Lineage K03.12 UCA antibody light chain	C	protein	214	Homo sapiens	Q6IPQ0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5W0D_1 Hemagglutinin HA1 (chains A)
ASAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQL
SSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYA
NNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGR
INYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGLEVLF

Sequence of entity 2 (B), FASTA

>5W0D_2 Lineage K03.12 UCA antibody heavy chain (chains B)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNY
AQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARDLTLMYVHSSGWERGVYYYYGM
DVWGQGTTVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALT
SGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHH
HHHH

Sequence of entity 3 (C), FASTA

>5W0D_3 Lineage K03.12 UCA antibody light chain (chains C)
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEGSKRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCCSYAGSVVFGGGTKLTVLGQPKGAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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 A7UPX0), best resolution first:

4HKX 2.5 Å, Influenza hemagglutinin in complex with CH67 Fab
4YJZ 2.72 Å, Human antibody H2526 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
5W6G 2.79 Å, Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
4YK4 2.8 Å, Human antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
9E6J 2.98 Å, DH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islands/3/2006
6Q0O 3.0 Å, human antibody H2227 lineage 652 in complex with influenza hemagglutinin head domain of…
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
6WIZ 4.2 Å, Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin
5UJZ 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK0 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK1 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK2 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…

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