3GBM: Fab CR6261

Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin. Determined by X-ray diffraction at 2.7 Å resolution. Released 10 Mar 2009.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Influenza A virus (A/Viet Nam/1203/2004(H5N1)), Homo sapiens
Chains: 8
Atoms: 14,189
Mol. weight: 213.73 kDa
Ligands: NAG, BMA
Released: 10 Mar 2009

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

Secondary structure: helices and β-sheets

3GBM contains 54 α-helices and 181 β-strands across 8 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, 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	51-54	4	7
β-strand	56	1	7
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-67	2
α-helix	68-72	5
α-helix	74-79	6
α-helix	82-83A	3
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	100-102	3	10
α-helix	105-112	8
β-strand	115-122	8	10
α-helix	125A-126	3
β-strand	131	1	11
β-strand	136-142	7	12
β-strand	144-146	3	12
β-strand	151-153	3	10
β-strand	155	1	11
β-strand	157	1	13
β-strand	160	1	13
α-helix	162-163	2
β-strand	164-169	6	14
β-strand	176-184	9	10
α-helix	188-195	8
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	223	1	15
β-strand	226	1	15
β-strand	229-237	9	10
β-strand	242-247	6	14
β-strand	251-254	4	10
β-strand	256-262	8	10
β-strand	267-269	3	8
β-strand	274-279	6	7
β-strand	281-283	3	16
β-strand	286-287	2	16
β-strand	294-295	2	6
β-strand	302-303	2	16
β-strand	307-308	2	6
β-strand	315-317	3	5
β-strand	321	1	4
α-helix	322-323	2

Chain B: 5 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	22-28	7	1
β-strand	31-36	6	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	146-154	9
α-helix	159-175	17

Chain C: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	18
β-strand	18	1	19
β-strand	25-26	2	20
β-strand	34-35	2	20
β-strand	36	1	21
β-strand	39-41	3	22
β-strand	43-44	2	23
β-strand	51-54	4	24
β-strand	59-60	2	25
β-strand	64	1	26
α-helix	66-70	5
α-helix	74-79	6
β-strand	87-89	3	25
β-strand	95	1	26
β-strand	100-102	3	27
α-helix	105-111	7
α-helix	112-114	3
β-strand	115-122	8	27
α-helix	125A-126	3
β-strand	131	1	28
β-strand	136-140	5	29
β-strand	145-146	2	29
β-strand	151-153	3	27
β-strand	155	1	28
β-strand	157	1	30
β-strand	160	1	30
α-helix	162-163	2
β-strand	164	1	31
β-strand	168-169	2	32
β-strand	176-184	9	27
α-helix	188-195	8
β-strand	202-205	4	31
β-strand	210-213	4	31
β-strand	223	1	33
β-strand	226	1	33
β-strand	229-237	9	27
β-strand	242-243	2	32
β-strand	244-247	4	31
β-strand	251-254	4	27
β-strand	256-262	8	27
β-strand	267-269	3	25
α-helix	272-273	2
β-strand	274-279	6	24
β-strand	281-283	3	34
β-strand	286-287	2	34
β-strand	294-295	2	23
β-strand	302-303	2	34
β-strand	307-308	2	23
β-strand	315-317	3	22
α-helix	320	1
β-strand	321	1	21
α-helix	322-323	2

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	35
β-strand	10	1	35
β-strand	14	1	19
β-strand	22-28	7	18
β-strand	31-36	6	18
α-helix	38-58	21
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	18
β-strand	137-140	4	18
α-helix	146-153	8
α-helix	159-170	12

Chain H: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	36
α-helix	7-9	3
β-strand	10-12	3	37
β-strand	18-24	7	36
β-strand	34-39	6	37
β-strand	45-51	7	37
β-strand	57-59	3	37
β-strand	67-72	6	36
β-strand	77-82	6	36
α-helix	84-86	3
β-strand	88-95	8	37
β-strand	100D-103	4	37
β-strand	107-111	5	37
α-helix	114-116	3
β-strand	117	1	38
α-helix	118-119	2
β-strand	120-124	5	39
β-strand	137-147	11	39
β-strand	148	1	38
β-strand	153-157	4	40
α-helix	162-164	3
β-strand	171-173	3	39
α-helix	174-176	3
β-strand	177-178	2	39
β-strand	185-194	10	39
α-helix	195-197	3
β-strand	207-212	6	40
β-strand	217-222	6	40

Chain I: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	48
β-strand	10-12	3	49
β-strand	17-24	8	48
β-strand	34-39	6	49
β-strand	46-51	6	49
β-strand	57-59	3	49
β-strand	67-72	6	48
α-helix	73-75	3
β-strand	77-82A	7	48
α-helix	84-86	3
β-strand	88-95	8	49
β-strand	100D-103	4	49
β-strand	107-111	5	49
β-strand	117	1	50
β-strand	120-124	5	51
α-helix	125	1
β-strand	138-147	10	51
β-strand	148	1	50
β-strand	153-157	4	52
α-helix	162-164	3
β-strand	171-173	3	51
α-helix	174-176	3
β-strand	177-178	2	51
β-strand	185-193	9	51
α-helix	196-198	3
β-strand	207-212	6	52
α-helix	213-215	3
β-strand	217-222	6	52

Chain L: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	41
β-strand	9-11	2	42
β-strand	18-24	7	41
α-helix	27-29	5
β-strand	33-38	6	42
β-strand	45-48	4	42
β-strand	49	1	43
β-strand	53	1	43
β-strand	63-65	3	41
β-strand	70-76	7	41
α-helix	80-82	3
β-strand	84-92	9	42
β-strand	95C-98	4	42
β-strand	102-104	3	42
β-strand	111	1	44
β-strand	114	1	45
β-strand	117-118	2	46
α-helix	122-126	5
β-strand	130-139	10	46
β-strand	140	1	44
β-strand	145-150	6	47
β-strand	153-155	3	47
β-strand	159-161	3	46
α-helix	162-164	3
β-strand	173-181	9	46
α-helix	183-187	5
β-strand	192-198	7	47
β-strand	203-209	7	47

Chain M: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	53
β-strand	9-12	3	54
α-helix	17-18	2
β-strand	19-24	6	53
β-strand	33-38	6	54
β-strand	45-48	4	54
β-strand	49	1	55
β-strand	53	1	55
β-strand	62-67	6	53
β-strand	70-75	6	53
α-helix	80-82	3
β-strand	84-91	8	54
β-strand	96-98	3	54
β-strand	102-105	4	54
β-strand	114	1	56
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	57
β-strand	159-161	3	57
α-helix	162-164	3
β-strand	165-166	2	57
β-strand	173-181	9	57
α-helix	183-187	5
β-strand	196	1	58
β-strand	205	1	58

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C	protein	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q6DQ33
Hemagglutinin	B, D	protein	177	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q6DQ33
antibody (Fab)	H, I	protein	226	Homo sapiens
antibody (Fab)	L, M	protein	221	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>3GBM_1 Hemagglutinin (chains A, C)
ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCS
VAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQI
IPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLW
GIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPN
DAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
LTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR

Sequence of entity 2 (B, D), FASTA

>3GBM_2 Hemagglutinin (chains B, D)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR

Sequence of entity 3 (H, I), FASTA

>3GBM_3 antibody (Fab) (chains H, I)
EVQLVESGAEVKKPGSSVKVSCKASGGPFRSYAISWVRQAPGQGPEWMGGIIPIFGTTKY
APKFQGRVTITADDFAGTVYMELSSLRSEDTAMYYCAKHMGYQVRETMDVWGKGTTVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 4 (L, M), FASTA

>3GBM_4 antibody (Fab) (chains L, M)
QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNDYVSWYQQLPGTAPKLLIYDNNKRPSGIP
DRFSGSKSGTSATLGITGLQTGDEANYYCATWDRRPTAYVVFGGGTKLTVLGAAAGQPKA
APSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNK
YAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
BMA	beta-D-mannopyranose	C6 H12 O6	2

Water and common crystallization additives (GOL, EDO) 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 Q6DQ33), best resolution first:

4FQI 1.71 Å, Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza virus hemagglutinin
4XNQ 2.0 Å, Antibody hemagglutinin Complexes
6CF5 2.04 Å, Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in…
4KDO 2.4 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDN 2.48 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDM 2.5 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus
4XNM 2.51 Å, Antibody Influenza H5 Complex
4XRC 2.74 Å, Antibody hemagglutinin Complexes
5A3I 2.89 Å, Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5…
6E3H 2.9 Å, Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin
4N5Z 2.95 Å, Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D,…
6E7G 3.09 Å, Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1…

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