6E56: Human antibody H2214

Human antibody H2214 in complex with influenza hemagglutinin A/Aichi/2/1968 (X-31) (H3N2). Determined by X-ray diffraction at 2.0 Å resolution. Released 22 May 2019.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 6
Atoms: 11,890
Mol. weight: 166.04 kDa
Ligands: NAG
Released: 22 May 2019

Explore 6E56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E56 contains 50 α-helices and 156 β-strands across 6 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, 33 β-strands

Element	Residues	Length	Sheet
β-strand	43-44	2	13
β-strand	51-54	4	14
β-strand	58-60	3	15
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	16
β-strand	86-89	4	15
β-strand	100-101	2	17
β-strand	102	1	18
α-helix	105-115	11
β-strand	117	1	16
β-strand	120-122	3	17
β-strand	130-131	2	19
β-strand	136-141	6	20
β-strand	144-146	3	20
β-strand	151-153	3	17
β-strand	155-156	2	19
β-strand	157	1	21
β-strand	160	1	21
β-strand	164-169	6	22
β-strand	176-184	9	17
α-helix	188-195	8
β-strand	201-205	5	22
β-strand	210-213	4	22
α-helix	220-222	3
β-strand	223	1	23
β-strand	226	1	23
β-strand	229-237	9	17
β-strand	242-249	8	22
β-strand	251-254	4	17
β-strand	256-259	4	17
β-strand	266-269	4	15
α-helix	272-273	2
β-strand	274-278	5	14
β-strand	281-283	3	24
β-strand	286-288	3	24
β-strand	294-295	2	13
β-strand	302-303	2	24
α-helix	306	1
β-strand	307-308	2	13

Chain D: 7 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	43-44	2	1
β-strand	51-52	2	2
β-strand	58-60	3	3
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	4
β-strand	86-89	4	3
β-strand	100-101	2	5
β-strand	102	1	6
α-helix	105-115	11
β-strand	117	1	4
β-strand	120-122	3	5
β-strand	130-131	2	7
β-strand	136-141	6	8
β-strand	144-146	3	8
β-strand	151-153	3	5
β-strand	155-156	2	7
β-strand	157	1	9
β-strand	160	1	9
β-strand	164-169	6	10
β-strand	176-184	9	5
α-helix	188-195	8
β-strand	201-205	5	10
β-strand	210-213	4	10
α-helix	220-222	3
β-strand	223	1	11
β-strand	226	1	11
β-strand	229-237	9	5
β-strand	242-249	8	10
β-strand	251-254	4	5
β-strand	256-259	4	5
β-strand	266-269	4	3
α-helix	272-273	2
β-strand	274-275	2	2
β-strand	281-283	3	12
β-strand	286-288	3	12
β-strand	294-295	2	1
β-strand	302-303	2	12
α-helix	306	1
β-strand	307-308	2	1

Chain G: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	30
β-strand	11-12	2	31
β-strand	18-25	8	30
α-helix	29-31	3
β-strand	34-39	6	32
β-strand	45-51	7	32
β-strand	58-60	3	32
α-helix	62-64	3
β-strand	68-73	6	30
β-strand	78-83	6	30
α-helix	88-90	3
β-strand	92-99	8	32
α-helix	100-101	2
β-strand	108	1	6
β-strand	116-119	4	32
β-strand	123-125	3	32
β-strand	126-127	2	31
β-strand	133	1	33
α-helix	134-135	2
β-strand	136-140	5	34
α-helix	144-146	3
β-strand	147-148	2	34
β-strand	151-161	11	34
β-strand	162	1	33
β-strand	167-170	4	35
β-strand	175	1	35
β-strand	179-181	3	34
α-helix	182-184	3
β-strand	185-186	2	34
β-strand	192-201	10	34
α-helix	202-204	3
β-strand	211-216	6	35
α-helix	217-219	3
β-strand	221-226	6	35

Chain H: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	10-12	3	26
β-strand	18-25	8	25
α-helix	29-31	3
β-strand	34-39	6	26
β-strand	45-51	7	26
β-strand	58-60	3	26
α-helix	62-64	3
β-strand	68-73	6	25
β-strand	78-83	6	25
α-helix	88-90	3
β-strand	92-99	8	26
α-helix	100-101	2
β-strand	108	1	18
β-strand	116-119	4	26
β-strand	123-127	5	26
α-helix	130-132	3
β-strand	133	1	27
α-helix	134-135	2
β-strand	136-140	5	28
α-helix	144-146	3
β-strand	147	1	28
β-strand	151-161	11	28
β-strand	162	1	27
β-strand	167-170	4	29
α-helix	171-173	3
β-strand	179-181	3	28
α-helix	182-184	3
β-strand	185-186	2	28
β-strand	192-201	10	28
α-helix	202-204	3
β-strand	211-216	6	29
α-helix	217-219	3
β-strand	221-226	6	29

Chain I: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	10-13	4	37
β-strand	19-25	7	36
β-strand	33-38	6	37
β-strand	45-49	5	37
β-strand	53-54	2	37
α-helix	55	1
β-strand	62-66	5	36
β-strand	70-75	6	36
α-helix	80-82	3
β-strand	85-93	9	37
β-strand	95-99	5	37
β-strand	103-107	5	37
β-strand	112	1	38
α-helix	113-114	2
β-strand	115-119	5	39
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	39
β-strand	141	1	38
β-strand	146-151	6	40
β-strand	154-155	2	40
α-helix	156	1
β-strand	160-164	5	39
α-helix	165-168	4
β-strand	174-183	10	39
α-helix	184-187	4
β-strand	193-198	6	40
β-strand	206-210	5	40

Chain J: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	41
β-strand	10-13	4	42
β-strand	19-25	7	41
β-strand	33-38	6	42
β-strand	45-49	5	42
β-strand	53-54	2	42
α-helix	55	1
β-strand	62-67	6	41
β-strand	70-75	6	41
α-helix	80-82	3
β-strand	85-93	9	42
β-strand	95-99	5	42
β-strand	103-107	5	42
β-strand	112	1	43
α-helix	113-114	2
β-strand	115-119	5	44
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	44
β-strand	141	1	43
β-strand	145-151	7	45
β-strand	154-155	2	45
α-helix	156	1
β-strand	160-164	5	44
α-helix	165-168	4
β-strand	174-183	10	44
α-helix	184-188	5
β-strand	192-199	8	45
β-strand	206-211	6	45

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, D	protein	290	Influenza A virus	P03437
antibody H2214 heavy chain	G, H	protein	253	Homo sapiens
antibody H2214 light chain, K1642	I, J	protein	215	Homo sapiens	Q6PIL8 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6E56_1 Hemagglutinin (chains A, D)
TNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSN
CYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTK
SGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTDQEQTSLYVQASGRVTVSTRRSQQTIIPN
IGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDT
CISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGGLEVLFQ

Sequence of entity 2 (G, H), FASTA

>6E56_2 antibody H2214 heavy chain (chains G, H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFNHYAMTWVRQAPGKGLEWVASSSGSGRSTYY
TDSVKGRFSVSRDNSKNTLYLQMNSLRAEDTAVYYCAKSSNYYGSGSYSPDDYYHMDVWG
QGTTVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGSSLEV
LFQGPLGHHHHHH

Sequence of entity 3 (I, J), FASTA

>6E56_3 antibody H2214 light chain, K1642 (chains I, J)
EIVMTQSPDTLSVSPGERATLSCRASESISSNLAWYQQKPGQVPRLLIYGASTRATGVPA
RFTGSGSGTEFTLTISSLQSEDFAVYYCQQYNNRLPYTFGQGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Water and common crystallization additives (ACT) are not listed.

Primary citation

Antibodies to a Conserved Influenza Head Interface Epitope Protect by an IgG Subtype-Dependent Mechanism. Watanabe, A., McCarthy, K.R., Kuraoka, M. et al. Cell (2019) 177:1124-1135.e16. DOI 10.1016/j.cell.2019.03.048 · PubMed

Other PDB entries of the same protein (UniProt P03437), best resolution first:

8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
8PJG 1.83 Å, F11 TCR in complex with Human Leukocyte Antigen class II allotype DR1 presenting P11T->R…
1QU1 1.9 Å, Crystal structure of EHA2 (23-185)
1PYW 2.1 Å, Human class II MHC protein HLA-DR1 bound to a designed peptide related to influenza…
3S5L 2.1 Å, Crystal structure of CD4 mutant bound to HLA-DR1
1J8H 2.4 Å, Crystal Structure of a Complex of a Human alpha/beta-T cell Receptor, Influenza HA…
3S4S 2.4 Å, Crystal structure of CD4 mutant bound to HLA-DR1
1HTM 2.5 Å, Structure of influenza haemagglutinin at the PH of membrane fusion
2VIU 2.5 Å, Influenza virus hemagglutinin
6XPX 2.6 Å, Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of…
1FYT 2.6 Å, Crystal structure of a complex of a human alpha/beta-T cell receptor, influenza ha…

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