3GBN: Fab CR6261

Crystal Structure of Fab CR6261 in Complex with the 1918 H1N1 influenza virus hemagglutinin. Determined by X-ray diffraction at 2.2 Å resolution. Released 10 Mar 2009.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Influenza A virus (A/Brevig Mission/1/1918(H1N1)), Homo sapiens
Chains: 4
Atoms: 6,618
Mol. weight: 105.9 kDa
Ligands: NAG, ETX
Released: 10 Mar 2009

Explore 3GBN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GBN contains 20 α-helices and 84 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: 7 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	56	1	8
β-strand	59-62	4	9
β-strand	64	1	10
α-helix	66-71	6
α-helix	74-79	6
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
β-strand	131	1	12
β-strand	136-140	5	13
β-strand	145-146	2	13
β-strand	151-153	3	11
β-strand	155	1	12
β-strand	164-169	6	14
β-strand	176-184	9	11
α-helix	190-195	6
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	229-237	9	11
α-helix	238	1
β-strand	242-247	6	14
β-strand	251-254	4	11
β-strand	256-262	7	11
β-strand	267-269	3	9
α-helix	273	1
β-strand	274-278	5	7
β-strand	281-283	3	15
β-strand	286-288	3	15
β-strand	294-295	2	6
β-strand	301	1	16
β-strand	302-303	2	15
β-strand	305	1	17
α-helix	306	1
β-strand	307-308	2	6
β-strand	315-317	3	5
β-strand	321	1	4

Chain B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	18
β-strand	10	1	18
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-58	21
α-helix	60-61	2
β-strand	62	1	17
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	146-154	9
α-helix	159-172	14

Chain H: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	19
α-helix	7-9	3
β-strand	10-12	3	20
β-strand	18-24	7	19
β-strand	34-39	6	20
β-strand	46-51	6	20
β-strand	57-59	3	20
β-strand	67-72	6	19
α-helix	73-75	3
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-95	8	20
β-strand	100D-103	4	20
β-strand	107-111	5	20
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-122	3	22
β-strand	143-147	5	22
β-strand	148	1	21
α-helix	174-176	3
β-strand	177-178	2	22
β-strand	185-187	3	22

Chain L: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	23
β-strand	5	1	24
β-strand	9-13	4	25
β-strand	19-24	6	24
α-helix	28-30	3
β-strand	33-38	6	25
β-strand	45-48	4	25
β-strand	49	1	26
β-strand	53	1	26
β-strand	62-67	6	24
β-strand	70-75	6	24
α-helix	80-82	3
β-strand	84-92	9	25
β-strand	95C-98	4	25
β-strand	99	1	23
β-strand	102-106	5	25
β-strand	132-139	8	27
β-strand	159-166	8	27
β-strand	173-179	7	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A	protein	331	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Q9WFX3
Hemagglutinin	B	protein	179	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Q9WFX3
Fab Heavy Chain	H	protein	226	Homo sapiens
Fab Lambda Light Chain	L	protein	221	Homo sapiens

Sequence of entity 1 (A), FASTA

>3GBN_1 Hemagglutinin (chains A)
ADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCN
IAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEI
FPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVL
WGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEP
GDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIH
PVTIGECPKYVRSTKLRMATGLRNIPSIQSR

Sequence of entity 2 (B), FASTA

>3GBN_2 Hemagglutinin (chains B)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVSGR

Sequence of entity 3 (H), FASTA

>3GBN_3 Fab Heavy Chain (chains H)
EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKY
APKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 4 (L), FASTA

>3GBN_4 Fab Lambda Light Chain (chains L)
QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIP
DRFSGSKSGTSATLGITGLQTGDEANYYCATWDRRPTAYVVFGGGTKLTVLGAAAGQPKA
APSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNK
YAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
ETX	2-ethoxyethanol	C4 H10 O2	1

Water and common crystallization additives (EDO, GOL, CL, UNL) are not listed.

Primary citation

Antibody recognition of a highly conserved influenza virus epitope. Ekiert, D.C., Bhabha, G., Elsliger, M.A. et al. Science (2009) 324:246-251. DOI 10.1126/science.1171491 · 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
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
1RD8 3.0 Å, Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

Browse more

3GBN is part of these collections:

Viruses

About this viewer

MolViewer shows 3GBN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.