4PY8: Fab 3.1

Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin. Determined by X-ray diffraction at 2.91 Å resolution. Released 21 May 2014.

Method: X-ray diffraction
Resolution: 2.91 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 4
Atoms: 7,222
Mol. weight: 104.68 kDa
Ligands: NAG, MLI
Released: 21 May 2014

Explore 4PY8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PY8 contains 27 α-helices and 91 β-strands across 4 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	51-53	3	7
β-strand	54	1	8
β-strand	57	1	8
α-helix	58-59	2
β-strand	60-61	2	9
β-strand	65	1	10
α-helix	67-72	6
α-helix	75-80	6
β-strand	85	1	11
β-strand	89-91	3	9
β-strand	97	1	10
β-strand	105	1	11
α-helix	108-115	8
β-strand	118-125	8	11
α-helix	129-132	4
β-strand	137	1	12
β-strand	143-148	6	13
β-strand	151-153	3	13
β-strand	158-160	3	11
β-strand	162	1	12
β-strand	164	1	14
β-strand	167	1	14
α-helix	169-170	2
β-strand	171-176	6	15
β-strand	183-191	9	11
α-helix	197-202	6
β-strand	209-212	4	15
β-strand	217-220	4	15
β-strand	236-244	9	11
α-helix	245	1
β-strand	249-254	6	15
β-strand	258-261	4	11
β-strand	263-269	7	11
β-strand	275-277	3	9
α-helix	281	1
β-strand	282-286	5	7
β-strand	289-291	3	16
β-strand	294-295	2	16
β-strand	302-303	2	6
β-strand	310-311	2	16
α-helix	314	1
β-strand	315-316	2	6
β-strand	323-325	3	5
β-strand	329	1	4

Chain B: 6 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	22-27	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	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	160-162	3
α-helix	163-171	9

Chain I: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-12	3	19
β-strand	18-24	7	18
α-helix	27-31	5
β-strand	34-39	6	19
β-strand	46-51	6	19
β-strand	58-60	3	19
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-99	8	19
β-strand	109-112	4	19
β-strand	116-120	5	19
β-strand	126	1	20
α-helix	127-128	2
β-strand	129-133	5	21
β-strand	142-150	9	21
β-strand	151	1	20
β-strand	156-159	4	22
α-helix	160-162	3
β-strand	164	1	22
β-strand	168-170	3	21
β-strand	174-175	2	21
β-strand	181-188	8	21
β-strand	200-205	6	22
α-helix	206-208	3
β-strand	210-215	6	22

Chain J: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-13	4	24
β-strand	19-25	7	23
β-strand	33-38	6	24
β-strand	45-49	5	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	84-90	7	24
α-helix	96	1
β-strand	97-98	2	24
β-strand	102-106	5	24
β-strand	111	1	25
β-strand	114-118	5	26
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	26
β-strand	140	1	25
β-strand	146-150	5	27
β-strand	153-154	2	27
β-strand	159-163	5	26
β-strand	173-182	10	26
α-helix	183-187	5
β-strand	191-196	6	27
β-strand	205-210	6	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A	protein	331	Influenza A virus	Q9WFX3
Hemagglutinin HA2 chain	B	protein	179	Influenza A virus	Q9WFX3
antibody 3.1 heavy chain	I	protein	219	Homo sapiens
antibody 3.1 light chain	J	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>4PY8_1 Hemagglutinin HA1 chain (chains A)
ADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCN
IAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEI
FPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVL
WGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEP
GDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIH
PVTIGECPKYVRSTKLRMATGLRNIPSIQSR

Sequence of entity 2 (B), FASTA

>4PY8_2 Hemagglutinin HA2 chain (chains B)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVSGR

Sequence of entity 3 (I), FASTA

>4PY8_3 antibody 3.1 heavy chain (chains I)
QVQLVQSGGGVVQPGRSLRLSCAASEFTFRMYATHWVRQAPGKGLEWVALISYDGSNKYY
ADSVKGRFTISRDNSMNTVYLQMNTLRPEDTAVYYCARDLGGYFIRGIMDVWGQGTLVTV
SSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 4 (J), FASTA

>4PY8_4 antibody 3.1 light chain (chains J)
ELQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
MLI	Malonate ion	C3 H2 O4	2

Primary citation

Alternative Recognition of the Conserved Stem Epitope in Influenza A Virus Hemagglutinin by a VH3-30-Encoded Heterosubtypic Antibody. Wyrzucki, A., Dreyfus, C., Kohler, I. et al. J Virol (2014) 88:7083-7092. DOI 10.1128/JVI.00178-14 · 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
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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