4NM8: Broadly neutralizing antibody CR8043

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin. Determined by X-ray diffraction at 4.0 Å resolution. Released 25 Dec 2013.

Method: X-ray diffraction
Resolution: 4.0 Å
Organisms: Influenza A virus (strain A/Hong Kong/1/1968 H3N2), Homo sapiens
Chains: 12
Atoms: 21,672
Mol. weight: 318.38 kDa
Ligands: NAG
Released: 25 Dec 2013

Explore 4NM8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NM8 contains 84 α-helices and 271 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, 39 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	130-131	2	10
β-strand	136-141	6	11
β-strand	144-146	3	11
β-strand	151-153	3	9
β-strand	155-156	2	10
β-strand	157	1	12
β-strand	160	1	12
β-strand	164-169	6	13
β-strand	176-184	9	9
α-helix	188-195	8
β-strand	202-205	4	13
β-strand	210-213	4	13
β-strand	223	1	14
β-strand	226	1	14
β-strand	229-237	9	9
β-strand	242-247	6	13
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	15
β-strand	286-288	3	15
β-strand	294-295	2	5
β-strand	302-304	3	15
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	16
β-strand	10	1	16
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-55	18
β-strand	61-62	2	15
α-helix	76-126	51
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-171	13

Chain C: 7 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	17
β-strand	18	1	18
β-strand	24-26	3	19
β-strand	34-36	3	19
β-strand	39-41	3	20
β-strand	43-44	2	21
β-strand	51-54	4	22
β-strand	58-60	3	23
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	24
β-strand	86-89	4	23
β-strand	100-101	2	25
α-helix	105-115	11
β-strand	117	1	24
β-strand	120-122	3	25
β-strand	130-131	2	26
β-strand	136-141	6	27
β-strand	144-146	3	27
β-strand	151-153	3	25
β-strand	155-156	2	26
β-strand	157	1	28
β-strand	160	1	28
β-strand	164-169	6	29
β-strand	176-184	9	25
α-helix	188-195	8
β-strand	201-205	5	29
β-strand	210-213	4	29
β-strand	223	1	30
β-strand	226	1	30
β-strand	229-237	9	25
β-strand	242-249	8	29
β-strand	251-254	4	25
β-strand	256-259	4	25
α-helix	260	1
β-strand	266-269	4	23
α-helix	272-273	2
β-strand	274-278	5	22
β-strand	281-283	3	31
β-strand	286-288	3	31
β-strand	294-295	2	21
β-strand	302-304	3	31
α-helix	306	1
β-strand	307-308	2	21
β-strand	315-317	3	20
β-strand	321	1	19

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	14	1	18
β-strand	22-28	7	17
β-strand	31-36	6	17
α-helix	38-56	19
β-strand	61-62	2	31
α-helix	76-126	51
β-strand	130-132	3	17
β-strand	137-140	4	17
α-helix	146-153	8
α-helix	159-170	12

Chain E: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	32
β-strand	18	1	33
β-strand	24-26	3	34
β-strand	34-36	3	34
β-strand	39-41	3	35
β-strand	43-44	2	36
β-strand	51-54	4	37
β-strand	58-60	3	38
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	39
β-strand	86-89	4	38
β-strand	100-101	2	40
α-helix	105-115	11
β-strand	117	1	39
β-strand	120-122	3	40
β-strand	130-134	5	40
β-strand	136-141	6	41
β-strand	144-146	3	41
β-strand	151-156	6	40
β-strand	157	1	42
β-strand	160	1	42
β-strand	164-169	6	43
β-strand	176-184	9	40
α-helix	188-195	8
β-strand	202-205	4	43
β-strand	210-213	4	43
β-strand	223	1	44
β-strand	226	1	44
β-strand	229-237	9	40
β-strand	242-247	6	43
β-strand	251-254	4	40
β-strand	256-259	4	40
α-helix	260	1
β-strand	266-269	4	38
α-helix	272-273	2
β-strand	274-278	5	37
β-strand	281-283	3	45
β-strand	286-288	3	45
β-strand	294-295	2	36
β-strand	302-304	3	45
α-helix	306	1
β-strand	307-308	2	36
β-strand	315-317	3	35
β-strand	321	1	34

Chain F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	14	1	33
β-strand	22-28	7	32
β-strand	31-36	6	32
α-helix	38-55	18
β-strand	61-62	2	45
α-helix	76-126	51
β-strand	130-132	3	32
β-strand	137-140	4	32
α-helix	146-153	8
α-helix	159-170	12

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	52
β-strand	10-12	3	53
β-strand	18-25	8	52
α-helix	29-31	3
β-strand	34-39	6	53
β-strand	45-51	7	53
β-strand	57-59	3	53
α-helix	61-63	3
β-strand	67-72	6	52
β-strand	77-82	6	52
α-helix	84-86	3
β-strand	88-95	8	53
β-strand	100D-103	4	53
β-strand	107-111	5	53
β-strand	117	1	54
α-helix	118-119	2
β-strand	120-124	5	55
β-strand	135-145	11	55
β-strand	146	1	54
β-strand	151-154	4	56
α-helix	155-157	3
β-strand	159	1	56
β-strand	163-165	3	55
α-helix	166-168	3
β-strand	169-170	2	55
β-strand	176-185	10	55
α-helix	186-188	3
β-strand	194-200	7	56
α-helix	201-203	3
β-strand	205-211	7	56

Chain I: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	63
β-strand	10-12	3	64
β-strand	18-25	8	63
α-helix	29-31	3
β-strand	34-39	6	64
β-strand	45-51	7	64
β-strand	57-59	3	64
β-strand	67-72	6	63
β-strand	77-82	6	63
α-helix	84-86	3
β-strand	88-95	8	64
β-strand	100D-103	4	64
β-strand	107-111	5	64
β-strand	117	1	65
α-helix	118-119	2
β-strand	120-123	4	66
β-strand	136-145	10	66
β-strand	146	1	65
β-strand	151-154	4	67
α-helix	155-157	3
β-strand	159	1	67
β-strand	163-165	3	66
α-helix	166-168	3
β-strand	169-170	2	66
β-strand	176-184	9	66
α-helix	186-188	3
β-strand	194-200	7	67
α-helix	201-203	3
β-strand	205-211	7	67

2 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	323	Influenza A virus (strain A/Hong Kong/1/1968 H3N2)	Q91MA7
Hemagglutinin HA2 Chain	B, D, F	protein	176	Influenza A virus (strain A/Hong Kong/1/1968 H3N2)	Q91MA7
Antibody CR8043, Light Chain	L, M, N	protein	220	Homo sapiens	P01834 (AlphaFold model)
Antibody CR8043, Heavy Chain	H, I, J	protein	230	Homo sapiens	S6C4S0 (AlphaFold model)

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

>4NM8_1 Hemagglutinin HA1 Chain (chains A, C, E)
ADPGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTL
IDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFT
WTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPS
TNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVIN
SNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACP
KYVKQNTLKLATGMRNVPEKQTR

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

>4NM8_2 Hemagglutinin HA2 Chain (chains B, D, F)
GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTN
EKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFE
KTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGV

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

>4NM8_3 Antibody CR8043, Light Chain (chains L, M, N)
DIQMTQSPDSLAVSLGERATINCKSSQSVFSSSTNKNYLAWYQQKPGQPPKVLIYWSSTR
ESGVPDRFSASGSGTDFTLTISSLQAADVAVYYCHQYYTAPWTFGQGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

>4NM8_4 Antibody CR8043, Heavy Chain (chains H, I, J)
QVQLVQSGAEVKKPGASVKLSCKASGYTFTAYSMHWVRQAPGQSLEWLGWINTAIGNTQY
SQKFQDRVTITRDTSARTSYMELSSLRSGDTAVYFCARGASWDARGWSGYWGKGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

A common solution to group 2 influenza virus neutralization. Friesen, R.H., Lee, P.S., Stoop, E.J. et al. Proc Natl Acad Sci U S A (2014) 111:445-450. DOI 10.1073/pnas.1319058110 · PubMed

Other PDB entries of the same protein (UniProt Q91MA7), best resolution first:

4FNK 1.9 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin
8IB1 1.95 Å, Structure of the LAH31 Fab bound to an influenza virus HA epitope peptide
5UMN 1.97 Å, Crystal structure of C05 VPGSGW mutant bound to H3 influenza hemagglutinin, HA1 subunit
6NHR 2.1 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2…
6OCB 2.1 Å, Crystal structure of FluA-20 Fab in complex with the head domain of H3 (A/Hong…
5VTZ 2.15 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
7QA4 2.19 Å, Crystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglutinin at 2.2 Angstrom
6BKM 2.2 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D…
6TZB 2.24 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in…
5VTV 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
5VU4 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
6BKQ 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D…

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