5VMF: Influenza hemagglutinin H1 mutant DH1D

Influenza hemagglutinin H1 mutant DH1D in complex with 6'SLN. Determined by X-ray diffraction at 2.35 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Chains: 6
Atoms: 12,548
Mol. weight: 176.87 kDa
Ligands: NAG
Released: 8 Nov 2017

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

Secondary structure: helices and β-sheets

5VMF contains 42 α-helices and 153 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: 9 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	8	1	2
β-strand	15-16	2	3
β-strand	24-25	2	3
β-strand	26	1	4
β-strand	29-31	3	5
β-strand	33-34	2	6
β-strand	41-44	4	7
β-strand	47	1	7
α-helix	48-49	2
β-strand	50-51	2	8
β-strand	55	1	9
α-helix	57-62	6
β-strand	76	1	10
β-strand	79-81	3	8
β-strand	87	1	9
β-strand	95	1	10
α-helix	98-104	7
β-strand	108-115	8	10
α-helix	119-122	4
β-strand	127	1	11
β-strand	132-137	6	12
β-strand	140-142	3	12
β-strand	147-149	3	10
β-strand	151	1	11
β-strand	153	1	13
β-strand	156	1	13
α-helix	158-159	2
β-strand	160-165	6	14
β-strand	171-180	10	10
α-helix	184-191	8
β-strand	198-201	4	14
β-strand	206-209	4	14
β-strand	219	1	15
β-strand	222	1	15
β-strand	225-233	9	10
α-helix	234	1
β-strand	238-243	6	14
β-strand	247-250	4	10
β-strand	252-258	7	10
β-strand	264-266	3	8
α-helix	270	1
β-strand	271-276	6	7
β-strand	278-279	2	16
β-strand	284	1	16
β-strand	291-292	2	6
β-strand	299-300	2	16
α-helix	303	1
β-strand	304-305	2	6
β-strand	312-314	3	5
β-strand	318	1	4

Chain B: 5 helices, 8 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	38-57	20
β-strand	64-65	2	16
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-134	5	1
β-strand	137-140	4	1
α-helix	146-154	9
α-helix	160-162	3

Chain C: 8 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	18
β-strand	8	1	19
β-strand	15-16	2	20
β-strand	24-25	2	20
β-strand	26	1	21
β-strand	29-31	3	22
β-strand	33-34	2	23
β-strand	41-44	4	24
β-strand	47	1	24
α-helix	48-49	2
β-strand	50-51	2	25
β-strand	55	1	26
α-helix	57-62	6
β-strand	76	1	27
β-strand	79-81	3	25
β-strand	87	1	26
β-strand	95	1	27
α-helix	98-104	7
β-strand	108-115	8	27
α-helix	119-122	4
β-strand	127	1	28
β-strand	132-137	6	29
β-strand	140-142	3	29
β-strand	147-149	3	27
β-strand	151	1	28
β-strand	153	1	30
β-strand	156	1	30
β-strand	160-165	6	31
β-strand	171-180	10	27
α-helix	184-191	8
β-strand	198-201	4	31
β-strand	206-209	4	31
β-strand	219	1	32
β-strand	222	1	32
β-strand	225-233	9	27
α-helix	234	1
β-strand	238-243	6	31
β-strand	247-250	4	27
β-strand	252-258	7	27
β-strand	264-266	3	25
α-helix	270	1
β-strand	271-276	6	24
β-strand	278-279	2	33
β-strand	284	1	33
β-strand	291-292	2	23
β-strand	299-300	2	33
α-helix	303	1
β-strand	304-305	2	23
β-strand	312-314	3	22
β-strand	318	1	21

Chains D and F: 5 helices, 8 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	38-57	20
β-strand	64-65	2	33
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	160-162	3

Chain E: 10 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	35
β-strand	8	1	36
β-strand	15-16	2	37
β-strand	24-25	2	37
β-strand	26	1	38
β-strand	29-31	3	39
β-strand	33-34	2	40
β-strand	41-44	4	41
β-strand	47	1	41
α-helix	48-49	2
β-strand	50-51	2	42
β-strand	55	1	43
α-helix	57-62	6
α-helix	65-67	3
β-strand	76	1	44
β-strand	79-81	3	42
β-strand	87	1	43
β-strand	95	1	45
α-helix	98-104	7
β-strand	108	1	44
β-strand	112-115	4	45
α-helix	119-122	4
β-strand	126-127	2	46
β-strand	129	1	45
β-strand	132-137	6	47
β-strand	140-142	3	47
β-strand	147-149	3	45
β-strand	151-152	2	46
β-strand	153	1	48
β-strand	156	1	48
α-helix	158-159	2
β-strand	160-165	6	49
β-strand	171-180	10	45
α-helix	184-191	8
β-strand	198-201	4	49
β-strand	206-209	4	49
β-strand	219	1	50
β-strand	222	1	50
β-strand	225-233	9	45
α-helix	234	1
β-strand	238-243	6	49
β-strand	247-250	4	45
β-strand	252-256	5	45
β-strand	258	1	44
β-strand	264-266	3	42
α-helix	270	1
β-strand	271-276	6	41
β-strand	278-279	2	51
β-strand	284-285	2	51
β-strand	291-292	2	40
β-strand	299-300	2	51
α-helix	303	1
β-strand	304-305	2	40
β-strand	312-314	3	39
β-strand	318	1	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A, C, E	protein	326	Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)	Q9WFX3
Hemagglutinin HA2	B, D, F	protein	191	Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)	Q9WFX3

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

>5VMF_1 Hemagglutinin HA1 (chains A, C, E)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGW
LLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKT
SSWPNHETTGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHH
PPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDLASRMNYYWTLLEPGDTIT
FEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIG
ECPKYVRSTKLRMATGLRNIPSIQSR

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

>5VMF_2 Hemagglutinin HA2 (chains B, D, F)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVKLES
MGVYQGALVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Determinant of receptor-preference switch in influenza hemagglutinin. Ni, F., Kondrashkina, E., Wang, Q. Virology (2017) 513:98-107. DOI 10.1016/j.virol.2017.10.010 · PubMed

Other PDB entries of the same protein (UniProt Q9WFX3), best resolution first:

4GXX 1.8 Å, Crystal structure of the "avianized" 1918 influenza virus hemagglutinin
5VMC 2.15 Å, Influenza hemagglutinin H1 mutant DH1 in complex with 6'SLN
3GBN 2.2 Å, Crystal Structure of Fab CR6261 in Complex with the 1918 H1N1 influenza virus…
5VMG 2.45 Å, Influenza hemagglutinin H1 mutant DH1E in complex with 6'SLN
4JUG 2.7 Å, Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G
4EEF 2.7 Å, Crystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918…
3LZF 2.8 Å, Crystal Structure of Fab 2D1 in Complex with the 1918 Influenza Virus Hemagglutinin
4JUH 2.81 Å, Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed…
1RUZ 2.9 Å, 1918 H1 Hemagglutinin
4PY8 2.91 Å, Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin
5VMJ 2.95 Å, Influenza hemagglutinin H1 mutant DH1E in complex with 3'SLN
1RD8 3.0 Å, Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

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