8U44: A/Solomon Islands/3/2006 H1 HA

CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06. Determined by electron microscopy at 3.41 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 3.41 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 12
Atoms: 17,028
Mol. weight: 359.9 kDa
Ligands: NAG
Released: 26 Jun 2024

Explore 8U44 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U44 contains 42 α-helices and 219 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.

Chains A, G and H: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	9
β-strand	15	1	10
β-strand	18	1	11
β-strand	25-26	2	12
β-strand	34-35	2	12
β-strand	36	1	13
β-strand	39-41	3	14
β-strand	51	1	15
β-strand	54	1	16
β-strand	56	1	16
α-helix	57-59	3
β-strand	61	1	17
β-strand	64	1	18
α-helix	66-70	5
α-helix	74-76	3
β-strand	84	1	19
β-strand	88-89	2	17
β-strand	95	1	18
β-strand	100-102	3	20
α-helix	105-111	7
β-strand	115	1	19
β-strand	151-152	2	21
β-strand	157	1	22
β-strand	160	1	22
β-strand	164	1	23
β-strand	167-170	4	23
β-strand	176-184	9	20
α-helix	188-194	7
β-strand	202-205	4	23
β-strand	212-213	2	23
β-strand	229-237	9	20
β-strand	241-247	7	23
β-strand	252	1	20
β-strand	253-254	2	21
β-strand	268-269	2	17
α-helix	272-273	2
β-strand	274	1	15
β-strand	281-283	3	24
β-strand	286-287	2	24
β-strand	294-295	2	25
β-strand	302-303	2	24
α-helix	306	1
β-strand	307-308	2	25
β-strand	315-317	3	14
β-strand	321	1	13

Chains B, I and J: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	26
β-strand	10	1	26
β-strand	14	1	11
β-strand	24	1	10
α-helix	38-57	20
β-strand	64	1	24
α-helix	66-68	3
α-helix	75-126	52
β-strand	130-132	3	27
α-helix	134-136	3
β-strand	137	1	9
β-strand	138-140	3	27
α-helix	146-154	9
α-helix	160-169	10

Chains S, U and V: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	28
β-strand	10-12	3	29
β-strand	20-23	4	28
β-strand	33-37	5	29
β-strand	45	1	29
β-strand	47-49	3	30
β-strand	56-58	3	30
β-strand	63	1	28
β-strand	66-71	6	28
β-strand	76-81	6	28
α-helix	86-88	3
β-strand	90-95	6	29
β-strand	98	1	31
β-strand	109	1	31
β-strand	111	1	29
β-strand	115-119	5	29

Chains T, W and X: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	13	1	33
β-strand	19-25	7	32
β-strand	33	1	34
β-strand	34-38	5	35
β-strand	45-49	5	35
β-strand	53-54	2	35
β-strand	62-67	6	32
β-strand	70-75	6	32
β-strand	85-87	3	35
β-strand	90	1	34
β-strand	106	1	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
05.GC.w2.3C10-H1_SI06 Heavy chain	S, U, V	protein	245	Homo sapiens
05.GC.w2.3C10-H1_SI06 Light chain	T, W, X	protein	235	Homo sapiens
Hemagglutinin HA1 chain	A, G, H	protein	368	Influenza A virus	A7Y8I1
Hemagglutinin HA2 chain	B, I, J	protein	237	Influenza A virus	A7Y8I1

Sequence of entity 1 (S, U, V), FASTA

>8U44_1 05.GC.w2.3C10-H1_SI06 Heavy chain (chains S, U, V)
METDTLLLWVLLLWVPGSTGDEVQLVQSGAEVKKPGSSVRVSCKASGGTFSAISWVRQAP
GQGLEWMGGIIPVFGTANYAQKFQGRVTITADDSTSTAYMEVSSLRSDDTAVYYCAREET
WKGATIGVMGIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRV
EPKSC

Sequence of entity 2 (T, W, X), FASTA

>8U44_2 05.GC.w2.3C10-H1_SI06 Light chain (chains T, W, X)
METDTLLLWVLLLWVPGSTGDDIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQHK
PGKAPKLLIFTASNLQSGVPSRFSGGGSGTDFTLTISSLQPEDFATYYCQQSYTSPRTFG
QGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

>8U44_3 Hemagglutinin HA1 chain (chains A, G, H)
MVLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADPGDTICIGYHANNSTDTVDT
VLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGNCSVAGWILGNPECELLISRESWSY
IVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHN
GESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHKENAYV
SVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSR
GFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLR
NIPSIQSR

Sequence of entity 4 (B, I, J), FASTA

>8U44_4 Hemagglutinin HA2 chain (chains B, I, J)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKIDSGGGGL
NDIFEAQKIEWHERLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Primary citation

Maturation of germinal center B cells after influenza virus vaccination in humans. McIntire, K.M., Meng, H., Lin, T.H. et al. J Exp Med (2024) 221. DOI 10.1084/jem.20240668 · 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…
6FYT 2.8 Å, Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38
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
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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