4HKX: Influenza hemagglutinin

Influenza hemagglutinin in complex with CH67 Fab. Determined by X-ray diffraction at 2.5 Å resolution. Released 21 Nov 2012.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 3
Atoms: 5,199
Mol. weight: 73.04 kDa
Ligands: NAG
Released: 21 Nov 2012

Explore 4HKX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HKX contains 25 α-helices and 71 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: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
β-strand	10-12	3	11
β-strand	18-25	8	10
β-strand	34-39	6	11
β-strand	46-51	6	11
β-strand	58-60	3	11
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	101	1	12
α-helix	106-108	3
β-strand	112	1	12
β-strand	115-116	2	11
β-strand	120-124	5	11
α-helix	127-129	3
β-strand	130	1	13
α-helix	131-132	2
β-strand	133-137	5	14
β-strand	144-145	2	14
β-strand	148-158	11	14
β-strand	159	1	13
β-strand	164-167	4	15
α-helix	168-170	3
β-strand	172	1	15
β-strand	176-178	3	14
α-helix	179-181	3
β-strand	182-183	2	14
α-helix	184	1
β-strand	189-198	10	14
α-helix	199-201	3
β-strand	208-213	6	15
α-helix	214-216	3
β-strand	218-223	6	15

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	16
β-strand	9-12	4	17
α-helix	17	1
β-strand	18-23	6	16
α-helix	27-29	3
β-strand	33-37	5	17
β-strand	44-45	2	17
β-strand	61-66	6	16
β-strand	69-74	6	16
α-helix	79-81	3
β-strand	83-91	9	17
β-strand	96-99	4	17
β-strand	103-107	5	17
β-strand	113	1	18
α-helix	114-115	2
β-strand	116-120	5	19
α-helix	121-123	3
α-helix	124-128	5
β-strand	132-141	10	19
β-strand	142	1	18
β-strand	147-152	6	20
β-strand	155-157	3	20
β-strand	161-163	3	19
α-helix	164-166	3
β-strand	167-168	2	19
β-strand	174-182	9	19
α-helix	184-188	5
β-strand	193-199	7	20
β-strand	202-208	7	20

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	54-55	2	1
β-strand	59	1	2
α-helix	61-66	6
α-helix	69-71	3
α-helix	75-76	2
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	114-118	5	4
α-helix	123-126	4
β-strand	131	1	5
β-strand	136-141	6	6
β-strand	144-146	3	6
β-strand	151-153	3	4
β-strand	155	1	5
β-strand	157	1	7
β-strand	160	1	7
β-strand	164-169	6	8
β-strand	175-184	10	4
α-helix	188-195	8
β-strand	202-205	4	8
β-strand	210-213	4	8
β-strand	223	1	9
β-strand	226	1	9
β-strand	229-237	9	4
α-helix	238	1
β-strand	242-247	6	8
β-strand	251-254	4	4
β-strand	257-261	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	E	protein	220	Influenza A virus	A7UPX0
CH67 heavy chain	A	protein	231	Homo sapiens
CH67 light chain	B	protein	214	Homo sapiens

Sequence of entity 1 (E), FASTA

>4HKX_1 Hemagglutinin HA1 (chains E)
ADPGYLLEAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYE
ELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPN
LSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKV
RDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRG

Sequence of entity 2 (A), FASTA

>4HKX_2 CH67 heavy chain (chains A)
QVQLVQSGAEVRKPGASVKVSCKASGYTFTDNYIHWVRQAPGQGLEWMGWIHPNSGATKY
AQKFEGWVTMTRDTSISTVYMELSRSRSDDTAVYYCARAGLEPRSVDYYFYGLDVWGQGT
AVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 3 (B), FASTA

>4HKX_3 CH67 light chain (chains B)
QSALTQPPSVSVAPGQTATITCGGNNIGRKRVDWFQQKPGQAPVLVVYEDSDRPSGIPER
FSDSNSGTTATLTISRVEAGDEADYYCQVWDSDSDHVVFGGGTKLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

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

Primary citation

Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Schmidt, A.G., Xu, H., Khan, A.R. et al. Proc Natl Acad Sci U S A (2013) 110:264-269. DOI 10.1073/pnas.1218256109 · PubMed

Other PDB entries of the same protein (UniProt A7UPX0), best resolution first:

5W0D 1.9 Å, Inferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza…
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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