6XQ2: Human antibody S8V2-37

Human antibody S8V2-37 in complex with the influenza hemagglutinin head domain of A/Texas/50/2012(H3N2). Determined by X-ray diffraction at 3.0 Å resolution. Released 19 May 2021.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Influenza A virus (A/Texas/50/2012(H3N2)), Homo sapiens
Chains: 6
Atoms: 10,890
Mol. weight: 164.75 kDa
Ligands: NAG
Released: 19 May 2021

Explore 6XQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XQ2 contains 38 α-helices and 147 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: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	51-54	4	1
β-strand	58-60	3	2
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	3
β-strand	86-89	4	2
β-strand	100-102	3	4
α-helix	105-115	11
β-strand	117	1	3
β-strand	120-122	3	4
β-strand	131	1	5
β-strand	136-141	6	6
β-strand	144-146	3	6
β-strand	151-153	3	4
β-strand	155	1	5
β-strand	157	1	7
β-strand	160	1	7
β-strand	164-168	5	8
β-strand	176-184	9	4
α-helix	188-195	8
β-strand	202-205	4	8
β-strand	210-213	4	8
β-strand	223	1	9
β-strand	226	1	9
β-strand	229-237	9	4
β-strand	243-247	5	8
β-strand	251-254	4	4
β-strand	256-259	4	4
β-strand	266-269	4	2
α-helix	272-273	2
β-strand	274-278	5	1
β-strand	281-283	3	10
β-strand	286-288	3	10
β-strand	294	1	11
β-strand	302	1	10
β-strand	307	1	11

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-14	5	19
β-strand	19-29	11	4
α-helix	32	1
β-strand	33-37	5	20
β-strand	45-46	2	20
β-strand	62-65	4	4
β-strand	68-75	8	4
β-strand	84-86	3	19
β-strand	87-90	4	20
α-helix	96	1
β-strand	97-98	2	20
β-strand	102-107	6	19
β-strand	111	1	21
α-helix	112-113	2
β-strand	114-118	5	22
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	22
β-strand	140	1	21
β-strand	145-150	6	23
β-strand	153-154	2	23
β-strand	159-163	5	22
α-helix	164-167	4
β-strand	173-182	10	22
α-helix	183-187	5
β-strand	191-197	7	23
β-strand	205-210	6	23

Chain C: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	12
β-strand	14-15	2	13
β-strand	21-28	8	12
α-helix	32-34	3
β-strand	37-42	6	14
β-strand	49-54	6	14
β-strand	61-63	3	14
β-strand	68	1	12
β-strand	71-76	6	12
β-strand	81-86	6	12
α-helix	91-93	3
β-strand	95-101	7	14
α-helix	102	1
β-strand	103-105	3	15
β-strand	108-111	4	15
β-strand	115	1	14
β-strand	119-121	3	14
β-strand	122-123	2	13
β-strand	129	1	16
α-helix	130-131	2
β-strand	132-136	5	17
β-strand	147-157	11	17
β-strand	158	1	16
β-strand	163-166	4	18
α-helix	167-169	3
β-strand	171	1	18
β-strand	175-177	3	17
α-helix	178-180	3
β-strand	181-182	2	17
β-strand	188-197	10	17
α-helix	198-200	3
β-strand	206-212	7	18
α-helix	213-215	3
β-strand	217-223	7	18

Chain D: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	51-54	4	24
β-strand	58-60	3	25
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	26
β-strand	86-89	4	25
β-strand	100-102	3	27
α-helix	105-115	11
β-strand	117	1	26
β-strand	120-122	3	27
β-strand	130-131	2	28
β-strand	136-141	6	29
β-strand	144-146	3	29
β-strand	151-153	3	27
β-strand	155-156	2	28
β-strand	164-168	5	30
β-strand	176-184	9	27
α-helix	188-195	8
β-strand	202-205	4	30
β-strand	210-213	4	30
β-strand	229-237	9	27
β-strand	243-247	5	30
β-strand	251-254	4	27
β-strand	256-258	3	27
β-strand	266-269	4	25
α-helix	272-273	2
β-strand	274-278	5	24
β-strand	281-283	3	31
β-strand	286-288	3	31
β-strand	294	1	32
β-strand	302	1	31
β-strand	307	1	32

Chain E: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-14	5	39
β-strand	19-29	11	27
α-helix	32-33	2
β-strand	34-38	5	39
β-strand	45-46	2	39
α-helix	54-56	3
β-strand	62-75	14	27
α-helix	80-82	3
β-strand	85-90	6	39
α-helix	96	1
β-strand	97-98	2	39
β-strand	99	1	27
β-strand	102-107	6	39
α-helix	108-110	3
β-strand	114-118	5	40
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	40
β-strand	145-150	6	41
β-strand	153-155	3	41
β-strand	159-163	5	40
α-helix	164-167	4
β-strand	173-182	10	40
α-helix	183-187	5
β-strand	192-197	6	41
β-strand	205-209	5	41

Chain F: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	33
β-strand	14-15	2	34
β-strand	20-28	9	33
β-strand	37-42	6	35
β-strand	48-54	7	35
β-strand	61	1	35
β-strand	68	1	33
β-strand	71-76	6	33
β-strand	81-87	7	33
α-helix	91-93	3
β-strand	95-104	10	35
β-strand	109-115	7	35
β-strand	119-121	3	35
β-strand	122-123	2	34
β-strand	129	1	36
β-strand	132-136	5	37
β-strand	147-157	11	37
β-strand	158	1	36
β-strand	162-166	5	38
α-helix	167-169	3
β-strand	171	1	38
β-strand	175-177	3	37
α-helix	178-180	3
β-strand	181-182	2	37
β-strand	188-197	10	37
β-strand	207-212	6	38
α-helix	213-215	3
β-strand	217-222	6	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, D	protein	291	Influenza A virus (A/Texas/50/2012(H3N2))	R4L1D1
antibody S8V2-37 heavy chain	C, F	protein	233	Homo sapiens
antibody S8V2-37 light chain	B, E	protein	214	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>6XQ2_1 Hemagglutinin (chains A, D)
TNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSN
CYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTH
LNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPN
IGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGK
CKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGGALEVLFQ

Sequence of entity 2 (C, F), FASTA

>6XQ2_2 antibody S8V2-37 heavy chain (chains C, F)
EVQLVESGGGLVQPGGSLRLSCEASGFTFSNYEMNWVRQAPGKGLEWLSYIRSSGTVTSY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARDLVYTGSYYGMDVWGQGTRVTV
SGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

Sequence of entity 3 (B, E), FASTA

>6XQ2_3 antibody S8V2-37 light chain (chains B, E)
AIQLTQSPSSLSASVGDRVTITCRTSQGISTPLAWYQHKPGKSPKLLIHDAFSLESGVPS
RFSGSGSGTDFSLTISSVQPEDFATYYCQQFYDYPITFGQGTRLEIRRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface. McCarthy, K.R., Lee, J., Watanabe, A. et al. mBio (2021) 12:e0114421-e0114421. DOI 10.1128/mBio.01144-21 · PubMed

Other PDB entries of the same protein (UniProt R4L1D1), best resolution first:

6E4X 2.25 Å, Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)
5W08 2.6 Å, A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab
6XPY 3.6 Å, Human antibody S1V2-58 in complex with the influenza hemagglutinin head domain of…
6XPR 4.09 Å, Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain…
6XPQ 4.2 Å, Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of…

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