5A3I: Hemagglutinin

Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5 Haemagglutinin. Determined by X-ray diffraction at 2.89 Å resolution. Released 22 Jul 2015.

Method: X-ray diffraction
Resolution: 2.89 Å
Organisms: INFLUENZA A VIRUS (A/VIETNAM/1203/2004(H5N1)), HOMO SAPIENS
Chains: 8
Atoms: 14,561
Mol. weight: 210.51 kDa
Ligands: NAG
Released: 22 Jul 2015

Explore 5A3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5A3I contains 52 α-helices and 187 β-strands across 8 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: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	8	1	2
β-strand	14-16	3	3
β-strand	24-26	3	3
β-strand	29-31	3	4
β-strand	33-34	2	5
β-strand	41-44	4	6
β-strand	47	1	6
β-strand	50-51	2	7
β-strand	55	1	8
α-helix	57-62	6
α-helix	73-75	3
β-strand	79-81	3	7
β-strand	87	1	8
β-strand	93-95	3	9
α-helix	98-104	7
β-strand	108-115	8	9
α-helix	119-121	3
β-strand	126	1	10
β-strand	132-137	6	11
β-strand	140-142	3	11
β-strand	147-149	3	9
β-strand	151	1	10
α-helix	158-159	2
β-strand	160-165	6	12
β-strand	172-180	9	9
α-helix	184-190	7
β-strand	198-201	4	12
β-strand	206-209	4	12
α-helix	211-213	3
β-strand	225-233	9	9
β-strand	238-243	6	12
β-strand	247-250	4	9
β-strand	252-259	8	9
β-strand	264-266	3	7
β-strand	271-276	6	6
β-strand	278-279	2	13
β-strand	284	1	13
β-strand	291-292	2	5
β-strand	299-300	2	13
α-helix	303	1
β-strand	304-305	2	5
β-strand	312-314	3	4
β-strand	318	1	3

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	14
β-strand	10	1	14
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	33-36	4	1
α-helix	38-61	24
α-helix	63-76	14
α-helix	83-126	44
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-154	9
β-strand	163	1	15
β-strand	165	1	15

Chain C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	46-52	7	17
β-strand	57-60	4	17
β-strand	69-73	5	16
α-helix	74-76	3
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-98	7	17
β-strand	114-115	2	17
β-strand	119-123	5	17
β-strand	129	1	18
β-strand	132-136	5	19
β-strand	147-157	11	19
β-strand	158	1	18
β-strand	163-166	4	20
β-strand	171	1	20
β-strand	175-177	3	19
α-helix	178-180	3
β-strand	181-182	2	19
β-strand	188-197	10	19
α-helix	198-202	5
β-strand	207-212	6	20
α-helix	213-215	3
β-strand	217-222	6	20

Chain D: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10	1	22
β-strand	13	1	23
β-strand	19-25	7	21
β-strand	30	1	24
β-strand	36	1	24
β-strand	38-43	6	22
α-helix	48	1
β-strand	49-54	6	22
β-strand	58-59	2	22
α-helix	60	1
β-strand	67-72	6	21
β-strand	75-80	6	21
α-helix	85-87	3
β-strand	89-95	7	22
α-helix	101	1
β-strand	102-103	2	22
β-strand	107-109	3	22
α-helix	110	1
β-strand	111	1	23
α-helix	112	1
β-strand	116	1	25
α-helix	117-118	2
β-strand	119-123	5	26
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	26
β-strand	145	1	25
β-strand	150-155	6	27
β-strand	159	1	27
β-strand	164-168	5	26
α-helix	169-172	4
β-strand	178-187	10	26
α-helix	188-191	4
β-strand	196-202	7	27
β-strand	210-215	6	27

Chain E: 6 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	28
β-strand	8	1	29
β-strand	15-16	2	30
β-strand	24-25	2	30
β-strand	26	1	31
β-strand	29-31	3	32
β-strand	34	1	33
β-strand	41-44	4	34
β-strand	47	1	34
α-helix	48-49	2
β-strand	50-51	2	35
β-strand	55	1	36
α-helix	57-62	6
α-helix	65-70	6
β-strand	79-81	3	35
β-strand	87	1	36
β-strand	93-95	3	37
α-helix	98-105	8
β-strand	108-115	8	37
β-strand	126	1	38
β-strand	132-137	6	39
β-strand	140-142	3	39
β-strand	147-149	3	37
β-strand	151	1	38
α-helix	158-159	2
β-strand	160-165	6	40
β-strand	172-180	9	37
α-helix	184-190	7
β-strand	198-201	4	40
β-strand	206-209	4	40
β-strand	225-233	9	37
β-strand	238-243	6	40
β-strand	247-250	4	37
β-strand	252-259	8	37
β-strand	264-266	3	35
β-strand	271-276	6	34
β-strand	278-279	2	41
β-strand	284-285	2	41
β-strand	291-292	2	33
β-strand	299-300	2	41
β-strand	304-305	2	33
β-strand	312-314	3	32
β-strand	318	1	31

Chain F: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	42
β-strand	10	1	42
β-strand	14	1	29
β-strand	22-28	7	28
β-strand	31-36	6	28
α-helix	38-76	39
α-helix	84-126	43
α-helix	127-129	3
β-strand	130-132	3	28
β-strand	137-140	4	28
α-helix	146-154	9
α-helix	159-162	4

Chain G: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	43
β-strand	10-12	3	44
β-strand	18-25	8	43
α-helix	29-31	3
β-strand	34-39	6	44
β-strand	46-52	7	44
β-strand	57-60	4	44
β-strand	65	1	45
β-strand	68	1	45
β-strand	69-73	5	43
α-helix	74-76	3
β-strand	78-83	6	43
α-helix	88-90	3
β-strand	92-98	7	44
β-strand	115	1	44
β-strand	119-123	5	44
α-helix	126-128	3
β-strand	129	1	46
β-strand	132-134	3	47
β-strand	147-157	11	47
β-strand	158	1	46
β-strand	163	1	48
β-strand	166	1	49
β-strand	171	1	49
β-strand	175-177	3	47
α-helix	178-180	3
β-strand	181-182	2	47
β-strand	188-197	10	47
β-strand	207	1	50
β-strand	208	1	49
β-strand	210-212	3	48
β-strand	217-219	3	48
β-strand	222	1	50

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	51
β-strand	10-13	4	52
β-strand	19-25	7	51
β-strand	30	1	53
β-strand	36	1	53
β-strand	38-43	6	52
β-strand	50-53	4	52
β-strand	59	1	52
β-strand	67-72	6	51
β-strand	75-80	6	51
α-helix	85-87	3
β-strand	89-95	7	52
α-helix	101	1
β-strand	102-103	2	52
β-strand	107-111	5	52
β-strand	116	1	54
α-helix	117-118	2
β-strand	119-123	5	55
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	55
β-strand	145	1	54
β-strand	149-155	7	56
β-strand	159	1	56
β-strand	164-168	5	55
α-helix	169-172	4
β-strand	178-187	10	55
α-helix	188-191	4
β-strand	196-203	8	56
β-strand	210-215	6	56

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, E	protein	328	INFLUENZA A VIRUS (A/VIETNAM/1203/2004(H5N1))	Q6DQ33
Hemagglutinin	B	protein	166	INFLUENZA A VIRUS (A/VIETNAM/1203/2004(H5N1))	A8UDR1
Anti-haemagglutinin HA1 FAB heavy chain	C, G	protein	230	HOMO SAPIENS
Anti-haemagglutinin HA1 FAB light chain	D, H	protein	219	HOMO SAPIENS
Hemagglutinin	F	protein	166	INFLUENZA A VIRUS (A/VIETNAM/1203/2004(H5N1))	A8UDR1

Sequence of entity 1 (A, E), FASTA

>5A3I_1 HEMAGGLUTININ (chains A, E)
DPDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVA
GWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIP
KSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGI
HHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVKGLSGRMEFFWTILKPNDA
INFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLT
IGECPKYVKSNRLVLAIGLRNSPQRETR

Sequence of entity 2 (B), FASTA

>5A3I_2 HEMAGGLUTININ (chains B)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEA

Sequence of entity 3 (C, G), FASTA

>5A3I_3 ANTI-HAEMAGGLUTININ HA1 FAB HEAVY CHAIN (chains C, G)
EVQLVQSGAEVKKPGESLKISCKGSGYSFSDYWIGWVRQMPGEGLEWMGIIYPASSEIRY
SPSFQGLVTISRDKSINTASLQWSSLKASDTAIYYCARHASCSARSCYWGPVDYWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 4 (D, H), FASTA

>5A3I_4 ANTI-HAEMAGGLUTININ HA1 FAB LIGHT CHAIN (chains D, H)
DIVMTQSPLSLPVSPGEPASISCRSSQSLLHGNGYNYLDWYLQKPGQSPRLLIYLGSNRA
SGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQALQTPLTFGGGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (F), FASTA

>5A3I_5 HEMAGGLUTININ (chains F)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGKEFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEA

Ligands and cofactors

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

Primary citation

Structures of Complexes Formed by H5 Influenza Hemagglutinin with a Potent Broadly Neutralizing Human Monoclonal Antibody. Xiong, X., Corti, D., Liu, J. et al. Proc Natl Acad Sci U S A (2015) 112:9430. DOI 10.1073/PNAS.1510816112 · 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
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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