4GMS: Heterosubtypic Fab S139/1

Crystal structure of heterosubtypic Fab S139/1 in complex with influenza A H3 hemagglutinin. Determined by X-ray diffraction at 2.95 Å resolution. Released 3 Oct 2012.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Influenza A virus, Mus musculus
Chains: 12
Atoms: 21,460
Mol. weight: 322.73 kDa
Ligands: NAG
Released: 3 Oct 2012

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

Secondary structure: helices and β-sheets

4GMS contains 75 α-helices and 261 β-strands across 12 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, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	18	1	2
β-strand	24-26	3	3
β-strand	34-36	3	3
β-strand	39-41	3	4
β-strand	43-44	2	5
β-strand	51-54	4	6
β-strand	58-60	3	7
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	8
β-strand	86-89	4	7
β-strand	100-101	2	9
α-helix	105-115	11
β-strand	117	1	8
β-strand	120-122	3	9
β-strand	130-134	5	9
β-strand	136-141	6	10
β-strand	144-146	3	10
β-strand	151-156	6	9
β-strand	157	1	11
β-strand	160	1	11
β-strand	164-169	6	12
β-strand	176-184	9	9
α-helix	188-195	8
β-strand	201-205	5	12
β-strand	210-213	4	12
β-strand	223	1	13
β-strand	226	1	13
β-strand	229-237	9	9
β-strand	242-249	8	12
β-strand	251-254	4	9
β-strand	256-259	4	9
α-helix	260	1
β-strand	266-269	4	7
α-helix	272-273	2
β-strand	274-278	5	6
β-strand	281-283	3	14
β-strand	286-288	3	14
β-strand	294-295	2	5
β-strand	302-305	4	14
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chains B and D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	15
β-strand	10	1	15
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-55	18
β-strand	60-62	3	14
α-helix	76-126	51
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-170	12

Chain C: 9 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	16
β-strand	18	1	17
β-strand	24-26	3	18
β-strand	34-36	3	18
β-strand	39-41	3	19
β-strand	43-44	2	20
β-strand	51-54	4	21
β-strand	58-60	3	22
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	23
β-strand	86-89	4	22
β-strand	100-101	2	24
α-helix	105-115	11
β-strand	117	1	23
β-strand	120-122	3	24
β-strand	130-134	5	24
β-strand	136-141	6	25
β-strand	144-146	3	25
β-strand	151-156	6	24
β-strand	157	1	26
β-strand	160	1	26
β-strand	164-169	6	27
β-strand	176-184	9	24
α-helix	188-195	8
β-strand	201-205	5	27
β-strand	210-213	4	27
β-strand	223	1	28
β-strand	226	1	28
β-strand	229-237	9	24
β-strand	242-249	8	27
β-strand	251-254	4	24
β-strand	256-259	4	24
α-helix	260	1
β-strand	266-269	4	22
α-helix	272-273	2
β-strand	274-278	5	21
β-strand	281-283	3	29
β-strand	286-287	2	29
β-strand	294-295	2	20
β-strand	302-305	4	29
α-helix	306	1
β-strand	307-308	2	20
β-strand	315-317	3	19
α-helix	320	1
β-strand	321	1	18
α-helix	322	1

Chain E: 8 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	31
β-strand	18	1	32
β-strand	24-26	3	33
β-strand	34-36	3	33
β-strand	39-41	3	34
β-strand	43-44	2	35
β-strand	51-54	4	36
β-strand	58-60	3	37
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	38
β-strand	86-89	4	37
α-helix	90	1
β-strand	100-101	2	39
α-helix	105-115	11
β-strand	117	1	38
β-strand	120-122	3	39
β-strand	130-134	5	39
β-strand	136-141	6	40
β-strand	144-146	3	40
β-strand	151-156	6	39
β-strand	157	1	41
β-strand	160	1	41
β-strand	164-169	6	42
β-strand	176-184	9	39
α-helix	188-195	8
β-strand	201-205	5	42
β-strand	210-213	4	42
β-strand	223	1	43
β-strand	226	1	43
β-strand	229-237	9	39
β-strand	242-249	8	42
β-strand	251-254	4	39
β-strand	256-259	4	39
α-helix	260	1
β-strand	266-269	4	37
α-helix	272-273	2
β-strand	274-278	5	36
β-strand	281-283	3	44
β-strand	286-287	2	44
β-strand	294-295	2	35
β-strand	302-305	4	44
α-helix	306	1
β-strand	307-308	2	35
β-strand	315-317	3	34
β-strand	321	1	33

Chain F: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	45
β-strand	10	1	45
β-strand	14	1	32
β-strand	22-28	7	31
β-strand	31-36	6	31
α-helix	38-55	18
β-strand	60-62	3	44
α-helix	76-126	51
α-helix	127-129	3
β-strand	130-132	3	31
β-strand	137-140	4	31
α-helix	146-153	8
α-helix	159-170	12

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	51
β-strand	10-12	3	52
β-strand	18-25	8	51
α-helix	29-31	3
β-strand	34-40	7	52
β-strand	44-52	9	52
β-strand	56-59	4	52
α-helix	61-63	3
β-strand	67-72	6	51
β-strand	77-82	6	51
α-helix	84-86	3
β-strand	88-95	8	52
β-strand	100A-103	4	52
β-strand	107-111	5	52
α-helix	114-116	3
β-strand	117	1	53
α-helix	118-119	2
β-strand	120-124	5	54
α-helix	125-127	3
β-strand	135-145	11	54
β-strand	146	1	53
β-strand	151-154	4	55
α-helix	155-157	3
β-strand	159	1	55
β-strand	163-165	3	54
α-helix	166-168	3
β-strand	169-171	3	54
β-strand	174-184	11	54
β-strand	194-199	6	55
α-helix	200-202	3
β-strand	204-209	6	55

Chain I: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	60
β-strand	10-11	2	61
β-strand	18-25	8	60
α-helix	29-31	3
β-strand	34-40	7	61
β-strand	44-52	9	61
β-strand	56-59	4	61
α-helix	61-63	3
β-strand	67-72	6	60
β-strand	77-82	6	60
α-helix	84-86	3
β-strand	88-95	8	61
β-strand	100A-103	4	61
β-strand	107-110	4	61
β-strand	117	1	62
β-strand	120-124	5	63
β-strand	135-143	9	63
β-strand	146	1	62
α-helix	155-157	3
β-strand	163-165	3	63
α-helix	166-168	3
β-strand	169	1	64
β-strand	176	1	64
β-strand	177-184	8	63
β-strand	199	1	65
β-strand	204	1	65

Chain J: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	71
β-strand	10-12	3	72
β-strand	18-25	8	71
α-helix	29-31	3
β-strand	34-40	7	72
β-strand	44-52	9	72
β-strand	56-59	4	72
α-helix	61-63	3
β-strand	67-72	6	71
β-strand	77-82	6	71
α-helix	84-86	3
β-strand	88-95	8	72
β-strand	100A-103	4	72
β-strand	107-111	5	72
α-helix	114-116	3
β-strand	117	1	73
α-helix	118-119	2
β-strand	120-124	5	74
β-strand	136-145	10	74
β-strand	146	1	73
β-strand	151-154	4	75
α-helix	155-157	3
β-strand	163-165	3	74
α-helix	166-168	3
β-strand	169-171	3	74
β-strand	174-183	10	74
β-strand	194-199	6	75
α-helix	200-202	3
β-strand	204-209	6	75

3 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	320	Influenza A virus	P03435
Hemagglutinin HA2 chain	B, D, F	protein	176	Influenza A virus	P03435
Fab S139/1 light chain	L, M, N	protein	214	Mus musculus
Fab S139/1 heavy chain	H, I, J	protein	225	Mus musculus

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

>4GMS_1 Hemagglutinin HA1 chain (chains A, C, E)
GATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILDGINCTLIDA
LLGDPHCDGFQNEKWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFINEGFNWTG
VTQNGGSSACKRGPDSGFFSRLNWLYKSGSTYPVQNVTMPNNDNSDKLYIWGVHHPSTDK
EQTNLYVQASGKVTVSTKRSQQTIIPNVGSRPWVRGLSSRISIYWTIVKPGDILVINSNG
NLIAPRGYFKMRTGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKITYGACPKYV
KQNTLKLATGMRNVPEKQTR

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

>4GMS_2 Hemagglutinin HA2 chain (chains B, D, F)
GIFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTN
EKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFE
KTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGV

Sequence of entity 3 (L, M, N), FASTA

>4GMS_3 Fab S139/1 light chain (chains L, M, N)
DIVMTQSQKFMSTSVGDRVSVTCKASQNVDTNVAWYQEKPGQSPKTLIYSASNRYSGVPD
RFTGSASGTDFTLTITNVQSEDLAEYFCQQYNSYPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 4 (H, I, J), FASTA

>4GMS_4 Fab S139/1 heavy chain (chains H, I, J)
QVQLQQSGTELKKPGASVKISCKATGYTFSSYWIEWIKQRPGHGLEWIGEILPEIGMTNY
NENFKGKATFTANTSSNTVYMQLSSLTSEDSAVYYCARPYDYSWFAYWGQGTLVTVSAAK
TTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Water and common crystallization additives (SO4, GOL, PG4) are not listed.

Primary citation

Heterosubtypic antibody recognition of the influenza virus hemagglutinin receptor binding site enhanced by avidity. Lee, P.S., Yoshida, R., Ekiert, D.C. et al. Proc Natl Acad Sci U S A (2012) 109:17040-17045. DOI 10.1073/pnas.1212371109 · PubMed

Other PDB entries of the same protein (UniProt P03435), best resolution first:

6R0E 1.91 Å, Structure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT
8IOD 2.59 Å, Cryo-EM structure of the PG-901-bound human melanocortin receptor 5 (MC5R)-Gs complex
8INR 2.73 Å, Cryo-EM structure of the alpha-MSH-bound human melanocortin receptor 5 (MC5R)-Gs complex
4O58 2.75 Å, Crystal structure of broadly neutralizing antibody F045-092 in complex with…
8IOC 2.86 Å, Cryo-EM structure of the gamma-MSH-bound human melanocortin receptor 3 (MC3R)-Gs complex
8JRV 3.3 Å, Cryo-EM structure of the glucagon receptor bound to glucagon and beta-arrestin 1
8JRU 3.5 Å, Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state

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