6OC3: FluA-20 Fab

Crystal structure of FluA-20 Fab in complex with the head domain of H1 (A/Solomon Islands/3/2006). Determined by X-ray diffraction at 2.85 Å resolution. Released 15 May 2019.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Homo sapiens, Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Chains: 6
Atoms: 10,038
Mol. weight: 148.95 kDa
Ligands: NAG
Released: 15 May 2019

Explore 6OC3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OC3 contains 41 α-helices and 138 β-strands across 6 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	34-39	8	3
β-strand	46-52	7	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-96	9	3
β-strand	102-103	2	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	115-116	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	194-200	7	6
α-helix	201-203	3
β-strand	205-211	7	6

Chain B: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	3
β-strand	19-25	7	7
β-strand	33-38	6	3
α-helix	43-44	2
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	3
α-helix	96	1
β-strand	97-98	2	3
β-strand	102-107	6	3
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-154	2	10
α-helix	155	1
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
β-strand	205-210	6	10

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	18-25	8	11
β-strand	34-39	8	3
β-strand	46-51	6	3
β-strand	57-59	3	3
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-96	9	3
β-strand	100H-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	12
α-helix	115-116	2
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-124	5	14
β-strand	137-145	9	14
β-strand	146	1	13
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	159	1	15
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-170	2	14
β-strand	176-183	8	14
α-helix	186-188	3
β-strand	194-200	7	15
α-helix	201-203	3
β-strand	205-211	7	15

Chain D: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	16
β-strand	10-14	5	3
β-strand	19-24	6	16
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	3
α-helix	96	1
β-strand	97-98	2	3
β-strand	102-107	6	3
β-strand	111	1	17
α-helix	112-113	2
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	153-154	2	19
α-helix	155	1
β-strand	159-163	5	18
α-helix	164-167	4
β-strand	173-182	10	18
α-helix	183-187	5
β-strand	191-197	7	19
β-strand	205-210	6	19

Chain E: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	54-55	2	20
β-strand	59	1	21
α-helix	61-66	6
α-helix	69-71	3
β-strand	80	1	22
β-strand	83-84	2	20
β-strand	91	1	21
β-strand	99	1	23
α-helix	102-110	9
β-strand	112	1	22
β-strand	115-119	5	23
β-strand	131	1	24
β-strand	136-141	6	25
β-strand	144-146	3	25
β-strand	151-153	3	23
β-strand	155	1	24
β-strand	157	1	26
β-strand	160	1	26
β-strand	164-169	6	27
β-strand	175-184	10	23
α-helix	188-195	8
β-strand	202-205	4	27
β-strand	210-213	4	27
β-strand	223	1	28
β-strand	226	1	28
β-strand	229-237	9	23
β-strand	242-247	6	27
β-strand	251-254	4	23
β-strand	256-260	5	23

Chain F: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	54-55	2	29
β-strand	59	1	30
α-helix	61-66	6
α-helix	69-71	3
β-strand	80	1	31
β-strand	83-84	2	29
β-strand	91	1	30
β-strand	99	1	32
α-helix	102-108	7
β-strand	112	1	31
β-strand	114-119	6	32
β-strand	131	1	33
β-strand	136-141	6	34
β-strand	144-146	3	34
β-strand	151-153	3	32
β-strand	155	1	33
β-strand	157	1	35
β-strand	160	1	35
β-strand	164-169	6	36
β-strand	175-184	10	32
α-helix	188-195	8
β-strand	202-205	4	36
β-strand	210-213	4	36
β-strand	223	1	37
β-strand	226	1	37
β-strand	229-237	9	32
β-strand	242-247	6	36
β-strand	251-254	4	32
β-strand	256-261	6	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of FluA-20 Fab	A, C	protein	235	Homo sapiens
Light chain of FluA-20 Fab	B, D	protein	214	Homo sapiens
Hemagglutinin	E, F	protein	227	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8I1

Sequence of entity 1 (A, C), FASTA

>6OC3_1 Heavy chain of FluA-20 Fab (chains A, C)
QVQLEESGPGLVKPSETLSLTCSVSGVSVTSDIYYWTWIRQPPGKGLEWIGYIFYNGDTN
YNPSLKSRVTMSIDTSKNEFSLRLTSVTAADTAVYFCARGTEDLGYCSSGSCPNHWGQGT
LVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Sequence of entity 2 (B, D), FASTA

>6OC3_2 Light chain of FluA-20 Fab (chains B, D)
DIVMTQSPSSLSASIGDRVTITCRPSQNIRSFLNWFQHKPGKAPKLLIYAASNLQSGVPS
RFSGSGSGTEFTLTIRSLQPEDFATYYCQQSYNTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, F), FASTA

>6OC3_3 Hemagglutinin (chains E, F)
APLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSS
VSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANN
KEKEVLVLWGVHHPPNIGDQRALYHKENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGRIN
YYWTLLEPGDTIIFEANGNLIAPRYAFALSRGSGLVPRGSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface. Bangaru, S., Lang, S., Schotsaert, M. et al. Cell (2019) 177:1136-1152.e18. DOI 10.1016/j.cell.2019.04.011 · 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…
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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