4EEF: Designed inhibitor protein F-HB80.4

Crystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918 influenza virus hemagglutinin. Determined by X-ray diffraction at 2.7 Å resolution. Released 27 Jun 2012.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Influenza A virus, Artificial Gene
Chains: 9
Atoms: 12,880
Mol. weight: 198.73 kDa
Released: 27 Jun 2012

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

Secondary structure: helices and β-sheets

4EEF contains 56 α-helices and 162 β-strands across 9 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, 46 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	1
β-strand	16-17	2	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	56	1	8
β-strand	59-60	2	9
β-strand	64	1	10
α-helix	66-71	6
α-helix	74-76	3
α-helix	79-81	3
β-strand	83A	1	11
β-strand	87-89	3	9
β-strand	95	1	10
β-strand	102	1	11
α-helix	105-112	8
β-strand	115-122	8	11
α-helix	125A-126	4
β-strand	131	1	12
β-strand	136-141	6	13
β-strand	144-146	3	13
β-strand	151-153	3	11
β-strand	155	1	12
β-strand	157	1	14
β-strand	160	1	14
β-strand	164-169	6	15
β-strand	176-184	9	11
α-helix	188-195	8
β-strand	202-205	4	15
β-strand	210-213	4	15
β-strand	223	1	16
β-strand	226	1	16
β-strand	229-237	9	11
α-helix	238	1
β-strand	242-247	6	15
β-strand	251-254	4	11
β-strand	256-262	7	11
β-strand	267-269	3	9
α-helix	272-273	2
β-strand	274-278	5	7
β-strand	281-282	2	17
β-strand	287-288	2	17
β-strand	294-295	2	6
β-strand	301	1	18
β-strand	302-303	2	17
β-strand	305	1	19
α-helix	306	1
β-strand	307-308	2	6
β-strand	315-317	3	5
β-strand	321	1	4

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	33-36	4	1
α-helix	40-57	18
α-helix	60-61	2
β-strand	62	1	19
β-strand	65	1	18
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	159-162	4
α-helix	163-167	5

Chain C: 9 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	20
β-strand	15-18	4	21
β-strand	25-26	2	22
β-strand	34-35	2	22
β-strand	36	1	23
β-strand	39-41	3	24
β-strand	43-44	2	25
β-strand	51-54	4	26
β-strand	56	1	26
α-helix	57-58	2
β-strand	59-62	4	27
β-strand	64	1	28
α-helix	66-71	6
α-helix	74-81	8
β-strand	83A	1	29
β-strand	87-89	3	27
β-strand	95	1	28
β-strand	102	1	29
α-helix	105-112	8
β-strand	115-122	8	29
β-strand	131	1	30
β-strand	136-141	6	31
β-strand	144-146	3	31
β-strand	151-153	3	29
β-strand	155	1	30
β-strand	157	1	32
β-strand	160	1	32
α-helix	162-163	2
β-strand	164-169	6	33
β-strand	176-184	9	29
α-helix	188-195	8
β-strand	202-205	4	33
β-strand	210-213	4	33
β-strand	223	1	34
β-strand	226	1	34
β-strand	229-237	9	29
α-helix	238	1
β-strand	242-247	6	33
β-strand	251-254	4	29
β-strand	256-262	7	29
β-strand	267-269	3	27
α-helix	273	1
β-strand	274-279	6	26
β-strand	281-282	2	35
β-strand	287	1	35
β-strand	294-295	2	25
β-strand	301	1	36
β-strand	302-303	2	35
β-strand	305	1	37
α-helix	306	1
β-strand	307-308	2	25
β-strand	315-317	3	24
β-strand	321	1	23

Chain D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	38
β-strand	10	1	38
β-strand	13-14	2	21
β-strand	22-24	3	21
β-strand	27-28	2	20
β-strand	31-32	2	20
β-strand	35-36	2	21
α-helix	40-58	19
β-strand	62	1	37
β-strand	65	1	36
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	20
β-strand	137-140	4	20
α-helix	146-153	8
α-helix	159-171	13

Chain E: 7 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	39
β-strand	18	1	40
β-strand	25-26	2	41
β-strand	34-35	2	41
β-strand	36	1	42
β-strand	39-41	3	43
β-strand	43-44	2	44
β-strand	51-53	3	45
β-strand	54	1	46
β-strand	56	1	46
α-helix	57-58	2
β-strand	59-60	2	47
β-strand	64	1	48
α-helix	66-71	6
α-helix	74-81	8
β-strand	83A	1	49
β-strand	87-89	3	47
β-strand	95	1	48
β-strand	102	1	49
α-helix	105-112	8
β-strand	115-122	8	49
β-strand	130-131	2	50
β-strand	136-141	6	51
β-strand	144-146	3	51
β-strand	151-153	3	49
β-strand	155-156	2	50
β-strand	157	1	52
β-strand	160	1	52
β-strand	164-169	6	53
β-strand	176-184	9	49
α-helix	188-194	7
β-strand	202-205	4	53
β-strand	210-213	4	53
β-strand	223	1	54
β-strand	226	1	54
β-strand	229-237	9	49
β-strand	242-247	6	53
β-strand	251-254	4	49
β-strand	256-262	7	49
β-strand	267-269	3	47
α-helix	272-273	2
β-strand	274-278	5	45
β-strand	281-282	2	55
β-strand	287	1	55
β-strand	294-295	2	44
β-strand	301	1	56
β-strand	302-303	2	55
β-strand	305	1	57
α-helix	306	1
β-strand	307-308	2	44
β-strand	315-317	3	43
β-strand	321	1	42

Chain F: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	58
β-strand	10	1	58
β-strand	14	1	40
β-strand	22-25	4	39
β-strand	34-36	3	39
α-helix	38-56	19
α-helix	60-61	2
β-strand	62	1	57
β-strand	65	1	56
α-helix	75-123	49
α-helix	127-129	3
β-strand	132-134	3	39
β-strand	137-139	3	39
α-helix	159-162	4
α-helix	163-165	3
α-helix	166-169	4

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	15-22	8
α-helix	38-40	3
α-helix	46-50	5
α-helix	51-53	3

Chain H: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-12	3
α-helix	13-22	10
α-helix	33-38	6
α-helix	46-50	5
α-helix	51-53	3

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A, C, E	protein	331	Influenza A virus	Q9WFX3
Hemagglutinin HA2 chain	B, D, F	protein	179	Influenza A virus	Q9WFX3
F-HB80.4, designed hemagglutinin binding protein	G, H, I	protein	74	Artificial Gene

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

>4EEF_1 Hemagglutinin HA1 chain (chains A, C, E)
ADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCN
IAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEI
FPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVL
WGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEP
GDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIH
PVTIGECPKYVRSTKLRMATGLRNIPSIQSR

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

>4EEF_2 Hemagglutinin HA2 chain (chains B, D, F)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVSGR

Sequence of entity 3 (G, H, I), FASTA

>4EEF_3 F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN (chains G, H, I)
MDYKDDDDKGSHMASTRGSGRPWKFSENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEE
VKKHYELEHHHHHH

Primary citation

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Whitehead, T.A., Chevalier, A., Song, Y. et al. Nat Biotechnol (2012) 30:543-548. DOI 10.1038/nbt.2214 · 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
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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