1RD8: 1918 Human H1 Hemagglutinin Precursor

Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0). Determined by X-ray diffraction at 3.0 Å resolution. Released 23 Mar 2004.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Influenza A virus
Chains: 6
Atoms: 12,082
Mol. weight: 176.67 kDa
Ligands: PO4, NAG
Released: 23 Mar 2004

Explore 1RD8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RD8 contains 42 α-helices and 142 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	12-19	8	1
β-strand	24-25	2	2
β-strand	35-35A	2	2
β-strand	36	1	3
β-strand	39-41	3	4
β-strand	43-44	2	5
β-strand	51-53	3	6
β-strand	54	1	7
β-strand	56	1	7
α-helix	57-58	2
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-70	5
α-helix	75-77	3
β-strand	84	1	10
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	102	1	11
α-helix	105-111	7
β-strand	115	1	10
β-strand	119-122	4	11
α-helix	125A-126	4
β-strand	130-131	2	12
β-strand	136-141	6	13
β-strand	144-146	3	13
β-strand	151-153	3	11
β-strand	155-156	2	12
β-strand	164-168	5	14
β-strand	175-184	10	11
α-helix	188-195	8
β-strand	202-206	5	14
β-strand	209-213	5	14
β-strand	223	1	15
β-strand	226	1	15
β-strand	229-237	9	11
α-helix	238	1
β-strand	243-247	5	14
β-strand	251-254	4	11
β-strand	256-260	5	11
β-strand	262	1	10
β-strand	267-269	3	8
α-helix	273	1
β-strand	274-278	5	6
β-strand	281-282	2	16
β-strand	287-288	2	16
β-strand	294-295	2	5
β-strand	302-303	2	16
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chain B: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	20-28	9	1
β-strand	31-36	6	1
α-helix	38-57	20
β-strand	65	1	16
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-171	13

Chain C: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12-19	8	17
β-strand	24-25	2	18
β-strand	35-35A	2	18
β-strand	36	1	19
β-strand	39-41	3	20
β-strand	43-44	2	21
β-strand	51-53	3	22
β-strand	54	1	23
β-strand	56	1	23
α-helix	57-58	2
β-strand	59-60	2	24
α-helix	66-70	5
α-helix	75-77	3
β-strand	84	1	25
β-strand	87-89	3	24
β-strand	102	1	26
α-helix	105-111	7
β-strand	115	1	25
β-strand	119-122	4	26
α-helix	125A-126	4
β-strand	130-131	2	27
β-strand	136-141	6	28
β-strand	144-146	3	28
β-strand	151-153	3	26
β-strand	155-156	2	27
β-strand	164-168	5	29
β-strand	175-184	10	26
α-helix	188-195	8
β-strand	202-206	5	29
β-strand	209-213	5	29
β-strand	223	1	30
β-strand	226	1	30
β-strand	229-237	9	26
α-helix	238	1
β-strand	243-247	5	29
β-strand	251-254	4	26
β-strand	256-260	5	26
β-strand	262	1	25
β-strand	267-269	3	24
α-helix	273	1
β-strand	274-278	5	22
β-strand	281-283	3	31
β-strand	286-288	3	31
β-strand	294-295	2	21
β-strand	302-303	2	31
α-helix	306	1
β-strand	307-308	2	21
β-strand	315-317	3	20
β-strand	321	1	19

Chains D and F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	17
β-strand	20-28	9	17
β-strand	31-36	6	17
α-helix	38-57	20
β-strand	65	1	31
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	17
β-strand	137-140	4	17
α-helix	146-153	8
α-helix	159-171	13

Chain E: 9 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12-19	8	32
β-strand	24-25	2	33
β-strand	35-35A	2	33
β-strand	36	1	34
β-strand	39-41	3	35
β-strand	43-44	2	36
β-strand	51-53	3	37
β-strand	54	1	38
β-strand	56	1	38
α-helix	57-58	2
β-strand	59-60	2	39
β-strand	64	1	40
α-helix	66-70	5
α-helix	75-77	3
β-strand	84	1	41
β-strand	87-89	3	39
β-strand	95	1	40
β-strand	102	1	42
α-helix	105-111	7
β-strand	115	1	41
β-strand	120-122	3	42
α-helix	125A-126	4
β-strand	130-131	2	43
β-strand	136-141	6	44
β-strand	144-146	3	44
β-strand	151-153	3	42
β-strand	155-156	2	43
β-strand	164-168	5	45
β-strand	175-184	10	42
α-helix	188-195	8
β-strand	202-206	5	45
β-strand	209-213	5	45
β-strand	223	1	46
β-strand	226	1	46
β-strand	229-237	9	42
α-helix	238	1
β-strand	243-247	5	45
β-strand	251-254	4	42
β-strand	256-260	5	42
β-strand	262	1	41
β-strand	267-269	3	39
α-helix	273	1
β-strand	274-278	5	37
β-strand	281-282	2	47
β-strand	287-288	2	47
β-strand	294-295	2	36
β-strand	302-303	2	47
α-helix	306	1
β-strand	307-308	2	36
β-strand	315-317	3	35
β-strand	321	1	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
hemagglutinin	A, C, E	protein	335	Influenza A virus	Q9WFX3
hemagglutinin	B, D, F	protein	182	Influenza A virus	Q9WFX3

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

>1RD8_1 hemagglutinin (chains A, C, E)
ADPGYLLEDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQL
GKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFE
KFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKE
VLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWT
LLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPF
QNIHPVTIGECPKYVRSTKLRMATGLRNIPSIQSR

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

>1RD8_2 hemagglutinin (chains B, D, F)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVRSLV
PR

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Structure of the Uncleaved Human H1 Hemagglutinin from the Extinct 1918 Influenza Virus. Stevens, J., Corper, A.L., Basler, C.F. et al. Science (2004) 303:1866-1870. DOI 10.1126/science.1093373 · 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…
5VMF 2.35 Å, Influenza hemagglutinin H1 mutant DH1D in complex with 6'SLN
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

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