6CF5: Hemagglutinin

Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with small molecule N-Cyclohexyltaurine. Determined by X-ray diffraction at 2.04 Å resolution. Released 4 Apr 2018.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Chains: 6
Atoms: 13,578
Mol. weight: 178.97 kDa
Ligands: NAG, NHE
Released: 4 Apr 2018

Explore 6CF5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CF5 contains 45 α-helices and 144 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: 10 helices, 41 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	43-44	2	6
β-strand	51-54	4	7
β-strand	56	1	7
α-helix	57-58	2
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	100-102	3	10
α-helix	105-112	8
β-strand	115-122	8	10
α-helix	125A-126	3
β-strand	131	1	11
β-strand	136-141	6	12
β-strand	144-146	3	12
β-strand	151-153	3	10
β-strand	155	1	11
β-strand	157	1	13
β-strand	160	1	13
α-helix	162-163	2
β-strand	164-169	6	14
β-strand	176-184	9	10
α-helix	188-195	8
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	223	1	15
β-strand	226	1	15
β-strand	229-237	9	10
α-helix	238	1
β-strand	242-247	6	14
β-strand	251-254	4	10
β-strand	256-262	8	10
β-strand	267-269	3	8
β-strand	274-279	6	7
β-strand	281-283	3	16
β-strand	286-288	3	16
β-strand	294-295	2	6
β-strand	302-303	2	16
α-helix	306	1
β-strand	307-308	2	6
β-strand	315-317	3	5
β-strand	321	1	4
α-helix	322-323	2

Chains B and F: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	17
β-strand	10	1	17
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-58	21
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-154	9
α-helix	159-174	16

Chains C and E: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	18
β-strand	18	1	19
β-strand	25-26	2	20
β-strand	34-35	2	20
β-strand	36	1	21
β-strand	39-41	3	22
β-strand	43-44	2	23
β-strand	51-54	4	24
β-strand	56	1	24
α-helix	57-58	2
β-strand	59-60	2	25
β-strand	64	1	26
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	25
β-strand	95	1	26
β-strand	100-102	3	27
α-helix	105-112	8
β-strand	115-122	8	27
α-helix	125A-126	3
β-strand	131	1	28
β-strand	136-141	6	29
β-strand	144-146	3	29
β-strand	151-153	3	27
β-strand	155	1	28
β-strand	157	1	30
β-strand	160	1	30
α-helix	162-163	2
β-strand	164-169	6	31
β-strand	176-184	9	27
α-helix	188-195	8
β-strand	202-205	4	31
β-strand	210-213	4	31
β-strand	223	1	32
β-strand	226	1	32
β-strand	229-237	9	27
β-strand	242-247	6	31
β-strand	251-254	4	27
β-strand	256-262	8	27
β-strand	267-269	3	25
β-strand	274-279	6	24
β-strand	281-283	3	33
β-strand	286-288	3	33
β-strand	294-295	2	23
β-strand	302-303	2	33
α-helix	306	1
β-strand	307-308	2	23
β-strand	315-317	3	22
α-helix	320	1
β-strand	321	1	21
α-helix	322-323	2

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	34
β-strand	10	1	34
β-strand	14	1	19
β-strand	22-28	7	18
β-strand	31-36	6	18
α-helix	38-58	21
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	18
β-strand	137-140	4	18
α-helix	146-154	9
α-helix	159-175	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C, E	protein	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q6DQ33
Hemagglutinin	B, D, F	protein	177	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q6DQ18

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

>6CF5_1 Hemagglutinin (chains A, C, E)
ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCS
VAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQI
IPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLW
GIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPN
DAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
LTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR

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

>6CF5_2 Hemagglutinin (chains B, D, F)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	3

Water and common crystallization additives (GOL, PEG) are not listed.

Primary citation

A small-molecule fragment that emulates binding of receptor and broadly neutralizing antibodies to influenza A hemagglutinin. Kadam, R.U., Wilson, I.A. Proc Natl Acad Sci U S A (2018) 115:4240-4245. DOI 10.1073/pnas.1801999115 · 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
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,…
6E7G 3.09 Å, Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1…

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