5W42: Human monoclonal antibody H3v-47

Crystal structure of human monoclonal antibody H3v-47 in complex with influenza virus hemagglutinin from A/Minnesota/11/2010 (H3N2). Determined by X-ray diffraction at 3.57 Å resolution. Released 25 Jul 2018.

Method: X-ray diffraction
Resolution: 3.57 Å
Organisms: Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2)), Influenza A virus, Homo sapiens
Chains: 4
Atoms: 7,573
Mol. weight: 110.49 kDa
Ligands: ZN, NAG
Released: 25 Jul 2018

Explore 5W42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W42 contains 27 α-helices and 88 β-strands across 4 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, 37 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	18	1	2
β-strand	24-26	3	3
β-strand	34-36	3	3
β-strand	39-41	3	4
β-strand	43-44	2	5
β-strand	50-54	5	6
β-strand	58-60	3	7
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	8
β-strand	86-89	4	7
β-strand	100-101	2	9
α-helix	105-115	11
β-strand	117	1	8
β-strand	120-122	3	9
β-strand	131	1	10
β-strand	136-140	5	11
β-strand	145-146	2	11
β-strand	151-153	3	9
β-strand	155	1	10
α-helix	162-163	2
β-strand	164-169	6	12
β-strand	175-184	10	9
α-helix	188-194	7
β-strand	202-205	4	12
β-strand	210-213	4	12
β-strand	223	1	13
β-strand	226	1	13
β-strand	229-237	9	9
β-strand	242-247	6	12
β-strand	251-254	4	9
β-strand	256-260	5	9
β-strand	266-269	4	7
α-helix	272	1
β-strand	273-278	6	6
β-strand	281-283	3	14
β-strand	286-288	3	14
β-strand	294-295	2	5
β-strand	302-303	2	14
α-helix	305-306	2
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	15
β-strand	10	1	15
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-55	18
β-strand	62	1	14
α-helix	76-125	50
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-152	7
α-helix	160-170	11

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	16
β-strand	10-12	3	17
β-strand	20	1	16
β-strand	22-23	2	16
α-helix	26-31	6
β-strand	34-40	7	17
β-strand	43-52	10	17
β-strand	56-58	3	17
α-helix	61-63	3
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-95	8	17
α-helix	98-99	2
β-strand	100J-103	4	17
β-strand	107-111	5	17
α-helix	115-116	2
β-strand	117	1	18
β-strand	120-124	5	19
β-strand	135-145	11	19
β-strand	146	1	18
β-strand	151-154	4	20
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-185	10	19
α-helix	188-190	3
β-strand	195-200	6	20
β-strand	205-210	6	20

Chain L: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
α-helix	17-18	2
β-strand	19-28	11	21
β-strand	33-38	6	22
α-helix	43-44	2
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-75	14	21
α-helix	80-82	3
β-strand	85-90	6	22
β-strand	96-97	2	22
β-strand	101-105	5	22
α-helix	106	1
β-strand	110	1	23
β-strand	113-117	5	24
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	24
β-strand	139	1	23
β-strand	144-149	6	25
β-strand	153	1	25
β-strand	158-162	5	24
α-helix	163-166	4
β-strand	172-181	10	24
α-helix	182-185	4
β-strand	190-196	7	25
β-strand	204-209	6	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A	protein	329	Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))	I0AXC3
Hemagglutinin	B	protein	174	Influenza A virus	I0AXC3
Fab H3v-47 heavy chain	H	protein	236	Homo sapiens	Q6N089 (AlphaFold model)
Fab H3v-47 light chain	L	protein	214	Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5W42_1 Hemagglutinin (chains A)
QKLPGSDNSMATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGRICNSPHQILD
GKNCTLIDALLGDPHCDDFQNKEWDLFVERSTAYSNCYPYYVPDYATLRSLVASSGNLEF
TQESFNWTGVAQDGSSYACRRGSVNSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIW
GVHHPGTDKDQTNLYVQASGRVIVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPG
DILLINSTGNLIAPRGYFKIQSGKSSIMRSDAHIDECNSECITPNGSIPNDKPFQNVNKI
TYGACPRYVKQNTLKLATGMRNVPEKQTR

Sequence of entity 2 (B), FASTA

>5W42_2 Hemagglutinin (chains B)
GIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQITGKLNRVIKKTN
EKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMSKLFE
RTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDIYRNEALNNRFQIK

Sequence of entity 3 (H), FASTA

>5W42_3 Fab H3v-47 heavy chain (chains H)
QVQLVQSGAEVKKPGSSVRVSCKASGDTFSSYSITWVRQAPGHGLQWMGGIFPIFGSTNY
AQKFDDRLTITTDDSSRTVYMELTSLRLEDTAVYYCARGASKVEPAAPAYSDAFDMWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Sequence of entity 4 (L), FASTA

>5W42_4 Fab H3v-47 light chain (chains L)
DIVMTQSPGTLSLSPGERATLSCRTSQGVSSSYLAWYQQKPGQAPRLLISGSSSRATGIP
DRFSGSGSGRDFTLTISRLEPEDSAVYYCQQYATSPTFGQGTRVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

A multifunctional human monoclonal neutralizing antibody that targets a unique conserved epitope on influenza HA. Bangaru, S., Zhang, H., Gilchuk, I.M. et al. Nat Commun (2018) 9:2669-2669. DOI 10.1038/s41467-018-04704-9 · PubMed

Other PDB entries of the same protein (UniProt I0AXC3), best resolution first:

5XRS 2.91 Å, Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin in complex…
5XRT 3.15 Å, Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin

Browse structure collections

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