7UMM: H1 Solomon Islands 2006 hemagglutinin

H1 Solomon Islands 2006 hemagglutinin in complex with Ab109. Determined by electron microscopy at 3.36 Å resolution. Released 23 Nov 2022.

Method: Electron microscopy
Resolution: 3.36 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Mus musculus
Chains: 9
Atoms: 18,147
Mol. weight: 319.65 kDa
Ligands: NAG
Released: 23 Nov 2022

Explore 7UMM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UMM contains 63 α-helices and 234 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, B and C: 7 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	37-39	3	1
β-strand	51-52	2	2
β-strand	55	1	2
β-strand	58-59	2	3
β-strand	63	1	4
α-helix	65-70	6
β-strand	83	1	5
β-strand	87-89	3	3
β-strand	95	1	4
β-strand	103	1	5
α-helix	106-114	9
β-strand	116-122	7	5
α-helix	127-130	4
β-strand	140-145	6	6
β-strand	148-150	3	6
β-strand	155-157	3	5
β-strand	161	1	7
β-strand	164	1	7
β-strand	168	1	8
β-strand	171-173	3	8
β-strand	180-188	9	5
α-helix	192-199	8
β-strand	206-209	4	8
β-strand	214-217	4	8
β-strand	227	1	9
β-strand	230	1	9
β-strand	233-241	9	5
β-strand	246-251	6	8
β-strand	255-258	4	5
β-strand	261-266	6	5
β-strand	272-274	3	3
β-strand	283-284	2	2
β-strand	286-287	2	10
β-strand	292-293	2	10
β-strand	299-300	2	11
β-strand	307-308	2	10
α-helix	311	1
β-strand	312-313	2	11
β-strand	320-322	3	1
α-helix	406-408	3
α-helix	409-441	33

Chains H, I and J: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	34
α-helix	7-9	3
β-strand	10-12	3	35
β-strand	18-25	8	34
β-strand	34-39	6	35
β-strand	45-52	8	35
β-strand	57-60	4	35
α-helix	62-64	3
β-strand	68-73	6	34
β-strand	78-83	6	34
α-helix	88-90	3
β-strand	92-99	8	35
β-strand	108-111	4	35
β-strand	115-119	5	35
α-helix	125-127	3
β-strand	128-132	5	36
β-strand	140-147	8	36
α-helix	151-152	2
β-strand	153-156	4	37
α-helix	157-159	3
β-strand	165-167	3	36
α-helix	168-170	3
β-strand	171-172	2	36
β-strand	178-184	7	36
β-strand	191	1	38
β-strand	194	1	38
β-strand	196-202	7	37
α-helix	203-205	3
β-strand	207-213	7	37

Chains L, M and N: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	49
β-strand	10-13	4	50
β-strand	19-25	7	49
β-strand	30-31	2	51
β-strand	34-35	2	51
β-strand	37-42	6	50
β-strand	48-53	6	50
β-strand	57-58	2	50
α-helix	59	1
β-strand	66-71	6	49
β-strand	74-79	6	49
α-helix	84-86	3
β-strand	89-94	6	50
β-strand	102	1	50
β-strand	107-110	4	50
β-strand	115	1	52
β-strand	118-122	5	53
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	53
β-strand	144	1	52
β-strand	149-154	6	54
β-strand	157-159	3	54
β-strand	163-167	5	53
α-helix	168-171	4
β-strand	177-186	10	53
α-helix	187-191	5
β-strand	195-201	7	54
β-strand	209-214	6	54

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, B, C	protein	523	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8I1
ab109 Fab heavy chain	H, I, J	protein	218	Mus musculus
ab109 Fab light chain	L, M, N	protein	218	Mus musculus

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

>7UMM_1 Hemagglutinin (chains A, B, C)
ADPGYLLEDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQL
GNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFE
RFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEV
LVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTL
LEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQ
NVHPVTIGECPKYVRSAKLRMVTGLRNIPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHH
QNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVDD
GFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCND
ECMESVKNGTYDYPKYSEESKLNREKIDGVRSGSGGALEVLFQ

Sequence of entity 2 (H, I, J), FASTA

>7UMM_2 ab109 Fab heavy chain (chains H, I, J)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYIHWVRQAPGQGLEWMGWINPNTGGTVY
AQTFQARVTMTRDTSISTAYMELIRLRSDDTAVYYCARERGTGAPDAFNIWGQGTLVTVS
GASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L, M, N), FASTA

>7UMM_3 ab109 Fab light chain (chains L, M, N)
DIVMTQSPASLAVSLGQRATISCRASKSVSTSGYSYIHWYQQKPGQPPKLLIYLATNLES
GVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHSRDTPYTFGGGTKLEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

An epitope-enriched immunogen expands responses to a conserved viral site. Caradonna, T.M., Ronsard, L., Yousif, A.S. et al. Cell Rep (2022) 41:111628-111628. DOI 10.1016/j.celrep.2022.111628 · 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…
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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