6FYT: Hemagglutinin

Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38. Determined by X-ray diffraction at 2.8 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Lama glama
Chains: 3
Atoms: 5,096
Mol. weight: 73.68 kDa
Ligands: NAG
Released: 7 Nov 2018

Explore 6FYT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FYT contains 13 α-helices and 62 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: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	18	1	2
β-strand	25-26	2	3
β-strand	34-35	2	3
β-strand	36	1	4
β-strand	39-41	3	5
β-strand	43-44	2	6
β-strand	51-54	4	7
β-strand	56	1	7
α-helix	57-58	2
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-71	6
α-helix	74-79	6
β-strand	84	1	10
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	102	1	10
α-helix	105-111	7
β-strand	115-122	8	10
β-strand	131	1	11
β-strand	136-141	6	12
β-strand	144-146	3	12
β-strand	151-153	3	10
β-strand	155	1	11
β-strand	157	1	13
β-strand	160	1	13
β-strand	164-169	6	14
β-strand	175-184	10	10
α-helix	188-195	8
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	223	1	15
β-strand	226	1	15
β-strand	229-237	9	10
β-strand	242-247	6	14
β-strand	251-254	4	10
β-strand	256-262	7	10
β-strand	267-269	3	8
α-helix	272-273	2
β-strand	274-279	6	7
β-strand	281-282	2	16
β-strand	287-288	2	16
β-strand	294-295	2	6
β-strand	302-303	2	16
α-helix	306	1
β-strand	307-308	2	6
β-strand	315-317	3	5
β-strand	321	1	4

Chain B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	17
β-strand	10	1	17
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	32-36	5	1
α-helix	38-57	20
β-strand	64-65	2	16
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-172	14

Chain I: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	11-12	2	19
β-strand	17-24	8	18
β-strand	33-39	7	20
β-strand	46-52	7	20
β-strand	57-59	3	20
β-strand	67-72	6	18
β-strand	77-82A	7	18
α-helix	84-86	3
β-strand	88-95	8	20
β-strand	101-103	3	20
β-strand	107-109	3	20
β-strand	110-111	2	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A	protein	330	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8I1
Hemagglutinin	B	protein	174	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8I1
Single domain antibody SD38	I	protein	124	Lama glama

Sequence of entity 1 (A), FASTA

>6FYT_1 Hemagglutinin (chains A)
ADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGNCS
VAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEI
FPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLW
GVHHPPNIGDQRALYHKENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLEPG
DTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHP
VTIGECPKYVRSAKLRMVTGLRNIPSIQSR

Sequence of entity 2 (B), FASTA

>6FYT_2 Hemagglutinin (chains B)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKID

Sequence of entity 3 (I), FASTA

>6FYT_3 Single domain antibody SD38 (chains I)
EVQLVESGGGLVQPGGSLRLSCAVSISIFDIYAMDWYRQAPGKQRDLVATSFRDGSTNYA
DSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYLCHVSLYRDPLGVAGGMGVYWGKGALV
TVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin. Laursen, N.S., Friesen, R.H.E., Zhu, X. et al. Science (2018) 362:598-602. DOI 10.1126/science.aaq0620 · PubMed

Other PDB entries of the same protein (UniProt A7Y8I1), best resolution first:

6CF7 2.72 Å, Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin in…
5UGY 2.8 Å, Influenza hemagglutinin in complex with a neutralizing antibody
9CU7 2.82 Å, Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus…
6OC3 2.85 Å, Crystal structure of FluA-20 Fab in complex with the head domain of H1 (A/Solomon…
9DBX 2.9 Å, Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza…
7UMM 3.36 Å, H1 Solomon Islands 2006 hemagglutinin in complex with Ab109
8U44 3.41 Å, CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06
7UMN 3.6 Å, H1 Solomon Islands 2006 hemagglutinin in complex with Ab36
6XSK 3.85 Å, Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with…
6WIZ 4.2 Å, Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin

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