5WKO: Antibody 27F3 heavy chain

Crystal structure of antibody 27F3 recognizing the HA from A/California/04/2009 (H1N1) influenza virus. Determined by X-ray diffraction at 3.49 Å resolution. Released 25 Oct 2017.

Method: X-ray diffraction
Resolution: 3.49 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 24
Atoms: 43,322
Mol. weight: 623.36 kDa
Released: 25 Oct 2017

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

Secondary structure: helices and β-sheets

5WKO contains 180 α-helices and 573 β-strands across 24 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: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	17-25	9	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-59	2	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82A	7	1
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	131-132	2	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-188	3
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	2
β-strand	19-25	7	6
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
β-strand	85-90	6	2
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	7
α-helix	112-113	2
β-strand	114-118	5	8
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	8
β-strand	140	1	7
β-strand	145-150	6	9
β-strand	153-154	2	9
β-strand	159-160	2	8
β-strand	163	1	8
α-helix	165-167	3
β-strand	173-182	10	8
α-helix	183-187	5
β-strand	191-197	7	9
β-strand	205-210	6	9

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	10
α-helix	7-9	3
β-strand	10-12	3	11
β-strand	18-24	7	10
β-strand	34-39	6	11
β-strand	46-51	6	11
β-strand	58-59	2	11
α-helix	61-63	3
β-strand	67-72	6	10
β-strand	77-82	6	10
β-strand	88-94	7	11
α-helix	99	1
β-strand	102-103	2	11
β-strand	107-111	5	11
β-strand	117	1	12
α-helix	118-119	2
β-strand	120-124	5	13
β-strand	131-132	2	13
β-strand	135-145	11	13
β-strand	146	1	12
β-strand	151-154	4	14
β-strand	159	1	14
β-strand	163-165	3	13
α-helix	166-168	3
β-strand	169-170	2	13
β-strand	176-185	10	13
α-helix	188-191	4
β-strand	194-200	7	14
α-helix	201-203	3
β-strand	205-211	7	14

Chain D: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	11
β-strand	19-25	7	15
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	15
β-strand	70-75	6	15
β-strand	85-90	6	11
α-helix	96	1
β-strand	97-98	2	11
β-strand	102-106	5	11
β-strand	111	1	16
α-helix	112-113	2
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	145-150	6	18
β-strand	153-154	2	18
β-strand	159-160	2	17
β-strand	163	1	17
α-helix	165-167	3
β-strand	173-182	10	17
α-helix	183-187	5
β-strand	191-197	7	18
β-strand	205-210	6	18

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
α-helix	7-9	3
β-strand	10-12	3	20
β-strand	18-25	8	19
β-strand	34-39	6	20
β-strand	46-51	6	20
β-strand	58-59	2	20
α-helix	61-63	3
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-94	7	20
β-strand	102-103	2	20
β-strand	107-111	5	20
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
β-strand	131-132	2	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151-154	4	23
β-strand	159	1	23
β-strand	163-165	3	22
α-helix	166-168	3
β-strand	169-170	2	22
β-strand	176-185	10	22
α-helix	186-188	3
β-strand	189	1	24
β-strand	192	1	24
β-strand	194-200	7	23
α-helix	201-203	3
β-strand	205-211	7	23

Chain F: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	10-13	4	20
β-strand	19-29	11	25
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-75	14	25
α-helix	80-82	3
β-strand	85-90	6	20
α-helix	96	1
β-strand	97-98	2	20
β-strand	102-106	5	20
β-strand	111	1	26
α-helix	112-113	2
β-strand	114-118	5	27
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	27
β-strand	140	1	26
β-strand	145-150	6	28
β-strand	153-154	2	28
β-strand	159-160	2	27
β-strand	163	1	27
α-helix	165-167	3
β-strand	173-182	10	27
α-helix	183-187	5
β-strand	191-197	7	28
β-strand	205-210	6	28

Chain G: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	29
α-helix	7-9	3
β-strand	10-12	3	30
β-strand	17-24	8	29
β-strand	34-39	6	30
β-strand	46-51	6	30
β-strand	58-59	2	30
α-helix	61-63	3
β-strand	67-72	6	29
β-strand	77-82A	7	29
β-strand	88-94	7	30
β-strand	102-103	2	30
β-strand	107-111	5	30
β-strand	117	1	31
α-helix	118-119	2
β-strand	120-124	5	32
β-strand	131-132	2	32
β-strand	135-145	11	32
β-strand	146	1	31
β-strand	151-154	4	33
β-strand	159	1	33
β-strand	163-165	3	32
α-helix	166-168	3
β-strand	169-170	2	32
β-strand	176-185	10	32
α-helix	186-188	3
β-strand	189	1	34
β-strand	192	1	34
β-strand	194-200	7	33
α-helix	201-203	3
β-strand	205-211	7	33

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-13	4	30
β-strand	19-25	7	35
β-strand	33-38	6	30
β-strand	45-49	5	30
β-strand	53-54	2	30
α-helix	55	1
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	85-90	6	30
α-helix	96	1
β-strand	97-98	2	30
β-strand	102-106	5	30
β-strand	111	1	36
α-helix	112-113	2
β-strand	114-118	5	37
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	37
β-strand	140	1	36
β-strand	145-150	6	38
β-strand	153-154	2	38
β-strand	163	1	37
α-helix	165-167	3
β-strand	173-182	10	37
α-helix	183-187	5
β-strand	191-197	7	38
β-strand	206-210	5	38

11 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
Antibody 27F3 heavy chain	A, C, E, G, I, K	protein	225	Homo sapiens	Q6N089 (AlphaFold model)
Antibody 27F3 light chain	B, D, F, H, J, L	protein	213	Homo sapiens	Q6P5S8 (AlphaFold model), Q9UL78 (AlphaFold model)
Hemagglutinin	M, N, O, S, T, U	protein	331	Influenza A virus	C3W5S1
Hemagglutinin	P, Q, R, V, W, X	protein	177	Influenza A virus	C5MVT7

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>5WKO_1 Antibody 27F3 heavy chain (chains A, C, E, G, I, K)
QVQLVQSGAEVKKPGSSVQVSCRASGGTFGNYAINWVRQAPGQGLEWMGGISPIFGPPKY
AQKFQGRVTISADISSSTAYMDLSSLSSDDTAVYYCARKLEPPYYFYSYMDVWGKGTTVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>5WKO_2 Antibody 27F3 light chain (chains B, D, F, H, J, L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTITRLEPEDFAVYYCQQYVSTPLTFGGGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 3 (M, N, O, S, T, U), FASTA

>5WKO_3 Hemagglutinin (chains M, N, O, S, T, U)
ADPGDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCN
IAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEI
FPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVL
WGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEP
GDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIH
PITIGKCPKYVKSTKLRLATGLRNIPSIQSR

Sequence of entity 4 (P, Q, R, V, W, X), FASTA

>5WKO_4 Hemagglutinin (chains P, Q, R, V, W, X)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYE
KVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDSGR

Primary citation

Antibody 27F3 Broadly Targets Influenza A Group 1 and 2 Hemagglutinins through a Further Variation in VH1-69 Antibody Orientation on the HA Stem. Lang, S., Xie, J., Zhu, X. et al. Cell Rep (2017) 20:2935-2943. DOI 10.1016/j.celrep.2017.08.084 · PubMed

Other PDB entries of the same protein (UniProt Q6N089 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HPY 1.5 Å, Crystal structure of RV144-elicited antibody CH59 in complex with V2 peptide
5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
3QCU 1.98 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3QCT 2.15 Å, Crystal structure of the humanized apo LT3015 anti-lysophosphatidic acid antibody Fab…
3MNV 2.4 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
3QCV 2.51 Å, Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic…
5XRQ 2.6 Å, Crystal structure of human monoclonal antibody H3v-47
2OQJ 2.8 Å, Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006

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