8YVL: Neuraminidase of A/California/04/2009 HIN1

Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab. Determined by electron microscopy at 2.47 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 2.47 Å
Organisms: Homo sapiens, Influenza A virus (A/California/04/2009(H1N1))
Chains: 12
Atoms: 19,161
Mol. weight: 309.52 kDa
Ligands: CA, NAG
Released: 2 Jul 2025

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

Secondary structure: helices and β-sheets

8YVL contains 49 α-helices and 216 β-strands across 12 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	85	1	1
α-helix	90	1
β-strand	91	1	2
α-helix	92-93	2
β-strand	96-102	7	3
α-helix	105-109	5
β-strand	115-124	10	4
β-strand	129-139	11	4
α-helix	143-145	3
β-strand	157-162	6	4
β-strand	173-177	5	4
β-strand	180-185	6	5
β-strand	190-196	7	5
β-strand	203-208	6	5
β-strand	211-217	7	5
β-strand	225	1	6
β-strand	230	1	5
β-strand	232-234	3	6
β-strand	235	1	1
β-strand	237-244	8	6
β-strand	252-259	8	6
β-strand	262-268	7	6
β-strand	277-284	8	7
β-strand	287-293	7	7
α-helix	301	1
β-strand	302-306	5	7
β-strand	312-316	5	7
β-strand	349-353	5	8
β-strand	356-361	6	8
β-strand	369-376	8	8
β-strand	389-399	11	8
β-strand	403-408	6	3
α-helix	410-413	4
β-strand	418	1	2
β-strand	419-429	11	3
β-strand	438-448	11	3
α-helix	466-468	3

Chain D: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	85	1	25
α-helix	90	1
β-strand	91	1	26
α-helix	92-93	2
β-strand	96-102	7	27
α-helix	105-109	5
β-strand	115-124	10	28
β-strand	129-139	11	28
α-helix	143-145	3
β-strand	157-162	6	28
β-strand	173-177	5	28
β-strand	180-185	6	29
β-strand	190-196	7	29
β-strand	203-208	6	29
β-strand	211-217	7	29
β-strand	225	1	30
β-strand	230	1	29
α-helix	231	1
β-strand	232-234	3	30
β-strand	235	1	25
β-strand	237-244	8	30
β-strand	252-259	8	30
β-strand	262-268	7	30
β-strand	277-284	8	31
β-strand	287-293	7	31
α-helix	301	1
β-strand	302-306	5	31
β-strand	312-316	5	31
β-strand	349-353	5	32
β-strand	356-361	6	32
β-strand	369-376	8	32
β-strand	389-399	11	32
β-strand	403-408	6	27
α-helix	410-413	4
β-strand	418	1	26
β-strand	419-429	11	27
β-strand	438-448	11	27
α-helix	466-468	3

Chains E, F, G and H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	33
β-strand	10-13	4	34
β-strand	19-25	7	33
α-helix	31-33	3
β-strand	34-39	6	34
β-strand	46-50	5	34
β-strand	54-55	2	34
α-helix	56	1
β-strand	63-68	6	33
β-strand	71-76	6	33
α-helix	81-83	3
β-strand	86-91	6	34
β-strand	97-98	2	34
β-strand	102-106	5	34

Chains I, J, K and L: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	41
β-strand	10-12	3	42
β-strand	17-24	8	41
α-helix	26-31	6
β-strand	33-39	7	42
β-strand	45-51	7	42
β-strand	58-60	3	42
β-strand	68-73	6	41
β-strand	78-84	7	41
α-helix	88-90	3
β-strand	92-99	8	42
β-strand	101-102	2	43
β-strand	106-107	2	43
β-strand	112-113	2	42
β-strand	117-121	5	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vasodilator-stimulated phosphoprotein,Neuraminidase	A, B, C, D	protein	466	Homo sapiens, Influenza A virus (A/California/04/2009(H1N1))	P50552 (AlphaFold model)
CAV-F34 kappa chain	E, F, G, H	protein	107	Homo sapiens
CAV-F34 heavy chain	I, J, K, L	protein	123	Homo sapiens

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

>8YVL_1 Vasodilator-stimulated phosphoprotein,Neuraminidase (chains A, B, C, D)
MEFGLSWIFLAAILKGVQCADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIE
AFVQELRKRGSLVPRGSGGVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFIS
CSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASA
CHDGINWLTIGISGPDSGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMT
DGPSDGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPW
VSFNQNLEYQIGYICSGVFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTK
SISSRKGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFW
VELIRGRPEENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTIDK

Sequence of entity 2 (E, F, G, H), FASTA

>8YVL_2 CAV-F34 kappa chain (chains E, F, G, H)
EIVLTQSPGTLSLSPGERATLSCRASQYISSMNLAWYQQKPGQAPRLLISAASSRATGIP
DRFSGSGSGTDFTLTISGLEPEDFAVYYCQKYGSPYTFGQGTKVEIK

Sequence of entity 3 (I, J, K, L), FASTA

>8YVL_3 CAV-F34 heavy chain (chains I, J, K, L)
EVQLVESGGGLVEPGGSLRLSCAASGLTFSTYEMNWVRQAPGKGLEWISHISSSGFAIYY
ADSVRGRFTISRDIAKQSLDLQMNSLRAEDTAVYYCARDYYNRDLGYSGMDVWGQGTTVT
VSS

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	9
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Neuraminidase of A/California/04/2009 HIN1 in complex with CAV-F34 Fab. Wang, X., Ge, J., Li, X. To be published.

Other PDB entries of the same protein (UniProt P50552 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1USE 1.3 Å, human VASP tetramerisation domain
2PBD 1.5 Å, Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*
1USD 1.7 Å, human VASP tetramerisation domain L352M
2PAV 1.8 Å, Ternary complex of Profilin-Actin with the Last Poly-Pro of Human VASP
3CHW 2.3 Å, Complex of Dictyostelium discoideum Actin with Profilin and the Last Poly-Pro of Human…
9UB1 2.35 Å, The structure of Myanmar_N2 and M6B12_Fab complex
9UAX 2.71 Å, The structure of Myanmar_N2 and AS4C_Fab complex
8GAT 3.0 Å, Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase…
8GAU 3.6 Å, Structure of human NDS.1 Fab and 1G01 Fab in complex with influenza virus neuraminidase…
1EGX Solution structure of the ena-vasp homology 1 (EVH1) domain of human…

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