5UK1: Hemagglutinin HA1

CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 3. Determined by electron microscopy at 4.8 Å resolution. Released 31 May 2017.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Influenza A virus, Homo sapiens
Chains: 9
Atoms: 17,547
Mol. weight: 257.5 kDa
Ligands: NAG
Released: 31 May 2017

Explore 5UK1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UK1 contains 39 α-helices and 211 β-strands across 9 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.

Chains A, C and E: 5 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	18	1	2
β-strand	21-22	2	3
β-strand	25-26	2	3
β-strand	30	1	2
β-strand	33-35	3	4
β-strand	37	1	5
β-strand	47-48	2	6
β-strand	51	1	6
α-helix	52-53	2
β-strand	54-55	2	7
β-strand	59	1	8
α-helix	61-66	6
β-strand	83-85	3	7
β-strand	91	1	8
β-strand	99	1	9
α-helix	102-108	7
β-strand	115	1	9
β-strand	118	1	10
α-helix	123-126	4
β-strand	130-131	2	11
β-strand	136-140	5	12
β-strand	145-146	2	12
β-strand	151-153	3	9
β-strand	155-156	2	11
β-strand	164-169	6	13
β-strand	175-184	10	9
α-helix	188-194	7
β-strand	202-205	4	13
β-strand	210-213	4	13
β-strand	229-237	9	9
β-strand	242-247	6	13
β-strand	251-254	4	9
β-strand	257	1	10
β-strand	258-260	3	9
β-strand	268-270	3	7
β-strand	279-280	2	6
β-strand	282-284	3	14
β-strand	287-289	3	14
β-strand	295	1	5
β-strand	303-305	3	14
β-strand	308	1	5
β-strand	316-318	3	4

Chains B, D and F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	506	1	15
β-strand	510	1	15
β-strand	522-528	7	1
β-strand	531-536	6	1
α-helix	538-556	19
β-strand	563-565	3	14
α-helix	575-625	51
β-strand	630-633	4	1
β-strand	637-640	4	1
α-helix	646-653	8
α-helix	663-669	7

Chains G and H: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-5	2	46
β-strand	10-13	4	47
β-strand	21-25	5	46
β-strand	34-38	5	48
β-strand	46-50	5	48
β-strand	54-55	2	48
β-strand	63-68	6	46
β-strand	71-76	6	46
α-helix	81-83	3
β-strand	85-87	3	47
β-strand	88-92	5	48
β-strand	98-100	3	48
β-strand	104-108	5	47
β-strand	129-132	4	49
β-strand	136-137	2	50
β-strand	141-149	9	49
α-helix	158	1
β-strand	159-164	6	51
β-strand	170-176	7	51
β-strand	182-184	3	51
β-strand	189	1	49
β-strand	192-197	6	49
β-strand	202-210	9	49
α-helix	212-214	3
β-strand	216-222	7	51
β-strand	241	1	51
β-strand	246-248	3	51
β-strand	249-250	2	50

Chain I: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-5	2	58
β-strand	10-13	4	59
β-strand	21-25	5	58
β-strand	34-38	5	60
β-strand	46-50	5	60
β-strand	54-55	2	60
β-strand	63-68	6	58
β-strand	71-76	6	58
α-helix	81-83	3
β-strand	85-87	3	59
β-strand	88-92	5	60
β-strand	98-100	3	60
β-strand	104-108	5	59
β-strand	129-132	4	61
β-strand	136-137	2	62
β-strand	141-149	9	61
α-helix	158	1
β-strand	159-164	6	63
β-strand	170-176	7	63
β-strand	182-184	3	63
β-strand	189	1	61
β-strand	192-197	6	61
β-strand	202-210	9	61
α-helix	212-214	3
β-strand	216-222	7	63
β-strand	228	1	42
β-strand	241	1	63
β-strand	246-248	3	63
β-strand	249-250	2	62

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))	A7UPX0
Hemagglutinin HA2	B, D, F	protein	173	Influenza A virus	A7UPX0
scFv	G, H, I	protein	266	Homo sapiens

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

>5UK1_1 Hemagglutinin HA1 (chains A, C, E)
EDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAG
WILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPK
ESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVH
HPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTLLEPGDTI
IFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTI
GECPKYVRSAKLRMVTGLRNIPS

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

>5UK1_2 Hemagglutinin HA2 (chains B, D, F)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKI

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

>5UK1_3 scFv (chains G, H, I)
EIVLTQSPGTLSLSPGERATLSCRASQSISGYYLTWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGISPVITFGGGTNVEIKGGGGGSGGGGS
GGGGSEVQLVESGGGLVQPGGSLRLSCAASGFTFNIYDMHWVRQAPGKGLEWVSGLTTGG
DTSYSGSVRGRFSISRENAKNSLYLQMNNLRAGDTAAYFCVRGVREVGATGGDPFYYAMA
VWGQGTTVTVSSASGSSGSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Primary citation

CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface. Liu, Y., Pan, J., Jenni, S. et al. J Mol Biol (2017) 429:1829-1839. DOI 10.1016/j.jmb.2017.05.011 · 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…
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…
5UK2 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…

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