8ZDW: Hemagglutinin

The cryoEM structure of H5N1 HA split from symmetric filament in conformation A. Determined by electron microscopy at 3.45 Å resolution. Released 25 Sept 2024.

Method: Electron microscopy
Resolution: 3.45 Å
Organisms: Influenza A virus (strain A/Vietnam/1203/2004 H5N1), Mus musculus
Chains: 12
Atoms: 22,602
Mol. weight: 345.8 kDa
Ligands: NAG
Released: 25 Sept 2024

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

Secondary structure: helices and β-sheets

8ZDW contains 54 α-helices and 279 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, C and H: 3 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	1
β-strand	18	1	2
β-strand	25-26	2	3
β-strand	34-35	2	3
β-strand	36	1	4
β-strand	39-41	3	5
β-strand	44	1	6
β-strand	51-53	3	7
β-strand	54	1	8
β-strand	56	1	8
β-strand	59-60	2	9
β-strand	64	1	10
α-helix	66-71	6
β-strand	87-89	3	9
β-strand	95	1	10
β-strand	100-102	3	11
α-helix	105-112	8
β-strand	115	1	12
β-strand	118-121	4	11
β-strand	131	1	13
β-strand	136-141	6	14
β-strand	144-146	3	14
β-strand	151-153	3	11
β-strand	155	1	13
β-strand	164-169	6	15
β-strand	176-184	9	11
α-helix	188-194	7
β-strand	202-206	5	15
β-strand	209-213	5	15
β-strand	223	1	16
β-strand	226	1	16
β-strand	229-237	9	11
β-strand	242-247	6	15
β-strand	251-254	4	11
β-strand	257-260	4	11
β-strand	262	1	12
β-strand	267-269	3	9
β-strand	274-278	5	7
β-strand	281-283	3	17
β-strand	286-288	3	17
β-strand	294-295	2	6
β-strand	302	1	17
β-strand	307-308	2	6
β-strand	315-317	3	5
β-strand	321	1	4

Chains B, D and I: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	18
β-strand	10	1	18
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	32-36	5	1
α-helix	38-58	21
α-helix	75-126	52
α-helix	127-129	3
β-strand	131-132	2	1
β-strand	137-139	3	1
α-helix	146-153	8
α-helix	160-172	13

Chains E, J and R: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	48
β-strand	10-12	3	38
β-strand	19-24	6	48
β-strand	30-31	2	49
β-strand	34-35	2	49
β-strand	37-42	6	38
β-strand	49-53	5	38
β-strand	57-58	2	38
β-strand	66-71	6	48
β-strand	74-79	6	48
β-strand	89-94	6	38
α-helix	100	1
β-strand	101	1	38
β-strand	107-109	3	38
β-strand	115	1	50
β-strand	120-121	2	51
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	51
β-strand	144	1	50
β-strand	149-154	6	52
β-strand	157-158	2	52
β-strand	163-165	3	51
α-helix	169-171	3
β-strand	177-186	10	51
α-helix	190-192	3
β-strand	195-201	7	52
α-helix	208	1
β-strand	209-214	6	52

Chains F, L and U: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	36
β-strand	18-23	6	37
β-strand	33-39	7	38
β-strand	45-52	8	38
β-strand	57-60	4	38
β-strand	69-73	5	37
β-strand	78-83	6	37
α-helix	88-90	3
β-strand	93-99	7	38
β-strand	107-110	4	38
β-strand	114-115	2	38
β-strand	116-118	3	36
β-strand	124	1	39
β-strand	127-131	5	40
α-helix	132-134	3
β-strand	143-152	10	40
β-strand	153	1	39
β-strand	158-161	4	41
α-helix	162-164	3
β-strand	171-172	2	40
β-strand	176-178	3	40
β-strand	181-190	10	40
β-strand	201-206	6	41
β-strand	211-216	6	41
α-helix	218-220	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C, H	protein	337	Influenza A virus (strain A/Vietnam/1203/2004 H5N1)	Q6DQ33
Hemagglutinin	B, D, I	protein	228	Influenza A virus (strain A/Vietnam/1203/2004 H5N1)	Q6DQ33
H5M9 Fab, light chain	E, J, R	protein	217	Mus musculus
Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain	F, L, U	protein	222	Mus musculus	U5LP42 (AlphaFold model)

Sequence of entity 1 (A, C, H), FASTA

>8ZDW_1 Hemagglutinin (chains A, C, H)
MEKIVLLFAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDL
DGVKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHL
LSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSY
NNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSG
RMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGA
INSSMPFHNIHPLTIGECPKYVKSNRLVLATGLRNSP

Sequence of entity 2 (B, D, I), FASTA

>8ZDW_2 Hemagglutinin (chains B, D, I)
QRERRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNK
VNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFH
DSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKRE
EISGVKLESIGIYQILSIYSTVASSLALAIMVAGLSLWMCSNGSLQCR

Sequence of entity 3 (E, J, R), FASTA

>8ZDW_3 H5M9 Fab, light chain (chains E, J, R)
DIVLTQSPGSLTVSLGQRATISCRASESVDNFGKSFMHWYQQKPGQSPKLLIYRASNREF
GIPARFNGSGSGTDFALTINPVEADDVATYFCQQSNEDPRTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 4 (F, L, U), FASTA

>8ZDW_4 Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain (chains F, L, U)
EVHLQQSGPELVKPGASVKMSCKTSGYTFTEYTIHWMKQSHGKSLEWIGGIFPNNGDTTY
NQKFKVRATLTVGRSSSTAYMDLRSLTSEDSAVYYCVRNYGSSYGYFDVWGAGTTVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites. Li, R., Gao, J., Wang, L. et al. Npj Viruses (2024) 2:48-48. DOI 10.1038/s44298-024-00059-9 · PubMed

Other PDB entries of the same protein (UniProt Q6DQ33), best resolution first:

4FQI 1.71 Å, Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza virus hemagglutinin
4XNQ 2.0 Å, Antibody hemagglutinin Complexes
6CF5 2.04 Å, Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in…
4KDO 2.4 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDN 2.48 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDM 2.5 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus
4XNM 2.51 Å, Antibody Influenza H5 Complex
3GBM 2.7 Å, Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.
4XRC 2.74 Å, Antibody hemagglutinin Complexes
5A3I 2.89 Å, Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5…
6E3H 2.9 Å, Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin
4N5Z 2.95 Å, Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D,…

Browse structure collections

About this viewer

MolViewer shows 8ZDW directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.