8GAU: Human NDS.1 Fab and 1G01 Fab

Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase from A/Indiana/10/2011 (H3N2v). Determined by electron microscopy at 3.6 Å resolution. Released 28 Feb 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, Influenza A virus (A/Indiana/10/2011(H3N2))
Chains: 5
Atoms: 6,604
Mol. weight: 149.63 kDa
Ligands: NAG
Released: 28 Feb 2024

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

Secondary structure: helices and β-sheets

8GAU contains 11 α-helices and 86 β-strands across 5 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, 37 β-strands

Element	Residues	Length	Sheet
α-helix	90	1
β-strand	91	1	1
α-helix	92-93	2
β-strand	97-102	6	1
α-helix	105-108	4
β-strand	115	1	2
β-strand	118-121	4	3
β-strand	124	1	4
β-strand	129	1	4
β-strand	130-134	5	3
β-strand	139	1	2
α-helix	143-145	3
β-strand	157	1	5
β-strand	158-162	5	3
α-helix	165-167	3
β-strand	176	1	5
β-strand	179-184	6	6
β-strand	189-195	7	6
β-strand	202-207	6	6
β-strand	210-216	7	6
β-strand	224	1	7
β-strand	229	1	6
β-strand	231-233	3	7
β-strand	236-244	9	7
β-strand	250-258	9	7
β-strand	261-267	7	7
β-strand	276	1	8
β-strand	280-283	4	9
β-strand	286-290	5	9
β-strand	292	1	8
β-strand	301-306	6	9
β-strand	311-316	6	9
β-strand	319	1	10
β-strand	352-356	5	11
β-strand	359-364	6	11
β-strand	372-379	8	11
β-strand	388	1	10
β-strand	391-403	13	11
β-strand	407	1	1
β-strand	410-413	4	1
β-strand	418-429	12	1
β-strand	439-448	10	1

Chain H: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
β-strand	6	1	13
β-strand	17-22	6	13
β-strand	25	1	12
β-strand	33	1	14
β-strand	36-38	3	15
β-strand	46-50	5	15
β-strand	58-59	2	15
β-strand	67-72	6	13
β-strand	77-82A	7	13
β-strand	88-90	3	16
β-strand	91-92	2	15
β-strand	95	1	14
α-helix	100-100B	3
β-strand	107-109	3	16

Chain L: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	17
β-strand	10-13	4	18
α-helix	17-19	3
β-strand	22-24	3	17
β-strand	34-37	4	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-63	2	20
β-strand	66-67	2	21
β-strand	70-71	2	21
β-strand	74-75	2	20
β-strand	85-86	2	18
β-strand	87	1	19
β-strand	102-106	5	18

Chain M: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	22
β-strand	18-21	4	23
β-strand	23-25	3	22
α-helix	29-31	3
β-strand	33-39	7	24
β-strand	45-51	7	24
β-strand	57-59	3	24
α-helix	61-63	3
β-strand	68-70	3	23
β-strand	79-82	4	23
β-strand	88-97	10	24
β-strand	100K-103	6	24
β-strand	108-109	2	24

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	25
β-strand	10-13	4	26
β-strand	19-24	6	25
β-strand	33-38	6	26
β-strand	44-49	6	26
β-strand	53-54	2	26
α-helix	55	1
β-strand	62-65	4	25
β-strand	70-75	6	25
β-strand	85-90	6	26
β-strand	98	1	26
β-strand	103-106	4	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vasodilator-stimulated phosphoprotein, Neuraminidase chimera	A	protein	466	Homo sapiens, Influenza A virus (A/Indiana/10/2011(H3N2))	G9LQ08, P50552 (AlphaFold model)
Fab NDS.1, heavy chain	H	protein	230	Homo sapiens
Fab NDS.1, light chain	L	protein	214	Homo sapiens
Fab 1G01, heavy chain	M	protein	240	Homo sapiens
Fab 1G01, light chain	N	protein	216	Homo sapiens

Sequence of entity 1 (A), FASTA

>8GAU_1 Vasodilator-stimulated phosphoprotein, Neuraminidase chimera (chains A)
MEFGLSWIFLAAILKGVQCADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIE
AFVQELRKRGSLVPRGSGGEYRNWSKPQCNITGFAPFSKDNSIRLSAGGDIWVTREPYVS
CDPDKCYQFALGQGTTLNNGHSNNTVHDRTPYRTLLMNELGVPFHLGTRQVCMAWSSSSC
HDGKAWLHVCITGNDNNATASFIYNGRLVDSIGSWSKNILRTQESECVCINGTCTVVMTD
GSASGKADTKILFVEEGKIVHISTLSGSAQHVEECSCYPRFPGVRCVCRDNWKGSNRPIV
DINVKNYSIVSSYVCSGLVGDTPRKSDSVSSSYCLDPNNEKGGHGVKGWAFDDGNDVWMG
RTINETLRLGYETFKVIEGWSKANSKLQTNRQVIVEKGDRSGYSGIFSVEGKSCINRCFY
VELIRGRKEETKVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI

Sequence of entity 2 (H), FASTA

>8GAU_2 Fab NDS.1, heavy chain (chains H)
QVQLRQWGAGLLKPSETLSLTCDVYGGSFNFYFWTWIRQPPGKGLEWLGEITHSGSATYI
PSLKSRVTLSVDTSKGQFSLKLTSVNVADTAVYYCAGLPIDYDTVHLGYYPMDVWGQGTP
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 3 (L), FASTA

>8GAU_3 Fab NDS.1, light chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQGIRNYLAWYQQKPGKVPKLLIYGASTLQSGVPS
RFSGSGSGTDFSLTISSLQPEDIATYFCQEYNNAPRTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (M), FASTA

>8GAU_4 Fab 1G01, heavy chain (chains M)
DEVQLVESGGRALRPGGSLRLSCAASGFKFDDYAMSWVRQVPGKGLEFVSGLNWNGDITA
YTDSVKGRFTVSRDNAKNSLYLHINSPKPEDTALYYCARTSSWGDYTRGPEPKITWYFDL
WGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Sequence of entity 5 (N), FASTA

>8GAU_5 Fab 1G01, light chain (chains N)
DDIQLTQSPSFLSASVGDRITITCRASQGIDGYLAWYQQRPGKAPNLLIYAASLLQSGVP
SRFSGSGYGTEFTLTISSLQPEDFATYYCQHLDSYPLFTFGPGTKVDIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Protective human monoclonal antibodies target conserved sites of vulnerability on the underside of influenza virus neuraminidase. Lederhofer, J., Tsybovsky, Y., Nguyen, L. et al. Immunity (2024) 57:574-586.e7. DOI 10.1016/j.immuni.2024.02.003 · PubMed

Other PDB entries of the same protein (UniProt G9LQ08), best resolution first:

8GAT 3.0 Å, Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase…

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