6Q0O: Human antibody H2227 lineage 652

human antibody H2227 lineage 652 in complex with influenza hemagglutinin head domain of A/Solomon Islands/3/2006(H1N1). Determined by X-ray diffraction at 3.0 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 3
Atoms: 5,162
Mol. weight: 75.61 kDa
Ligands: NAG
Released: 18 Dec 2019

Explore 6Q0O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q0O contains 18 α-helices and 68 β-strands across 3 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: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	52-53	2
β-strand	54-55	2	1
β-strand	59	1	2
α-helix	61-66	6
β-strand	80	1	3
β-strand	83-84	2	1
β-strand	91	1	2
β-strand	99	1	4
α-helix	102-108	7
β-strand	112	1	3
β-strand	114-119	6	4
α-helix	123-126	4
β-strand	131	1	5
β-strand	133	1	4
β-strand	136-140	5	6
β-strand	145-146	2	6
β-strand	151-153	3	4
β-strand	155	1	5
β-strand	157	1	7
β-strand	160	1	7
β-strand	164-169	6	8
β-strand	175-184	10	4
α-helix	188-195	8
β-strand	202-205	4	8
β-strand	210-213	4	8
β-strand	223	1	9
β-strand	226	1	9
β-strand	229-237	9	4
β-strand	242-247	6	8
β-strand	251-254	4	4
β-strand	256-261	6	4

Chain B: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	10
β-strand	9-12	4	11
β-strand	18-23	6	10
α-helix	25-28	4
β-strand	33-37	5	11
β-strand	44-47	4	11
β-strand	61-65	5	10
β-strand	69-74	6	10
α-helix	79-81	3
β-strand	84-90	7	11
β-strand	98-100	3	11
β-strand	104-108	5	11
β-strand	119-121	3	12
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-140	8	12
β-strand	148-153	6	13
β-strand	157-158	2	13
β-strand	162-164	3	12
α-helix	165-167	3
β-strand	168-169	2	12
β-strand	175-183	9	12
α-helix	185-190	6
β-strand	194-200	7	13
β-strand	203-209	7	13

Chain Z: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	17-25	9	14
β-strand	34-40	7	16
β-strand	47-53	7	16
β-strand	57-60	4	16
α-helix	65-67	3
β-strand	68-73	6	14
β-strand	78-84	7	14
α-helix	88-90	3
β-strand	92-99	8	16
α-helix	110-112	3
β-strand	119-120	2	16
β-strand	124-126	3	16
β-strand	127-128	2	15
α-helix	131-133	3
β-strand	134	1	17
β-strand	137-141	5	18
β-strand	149	1	18
β-strand	152-162	11	18
β-strand	163	1	17
β-strand	168-171	4	19
β-strand	180-182	3	18
α-helix	183-185	3
β-strand	186-187	2	18
β-strand	193-202	10	18
α-helix	203-205	3
β-strand	212-217	6	19
α-helix	218-220	3
β-strand	222-227	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin head domain	A	protein	223	Influenza A virus	A7UPX0
H2227 Fab lambda chain	B	protein	214	Homo sapiens
H2227 Fab heavy chain	Z	protein	241	Homo sapiens

Sequence of entity 1 (A), FASTA

>6Q0O_1 Hemagglutinin head domain (chains A)
ASAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQL
SSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYA
NNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGR
INYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGLEVLF

Sequence of entity 2 (B), FASTA

>6Q0O_2 H2227 Fab lambda chain (chains B)
SELTQDPAVSVALGQTVRITCQGDSLRGYYASWHQQKPGQAPVLVIYGKNNRPSGIPDRF
SGSRSGNTASLTITGAQAEDEADYYCASRDSSGNHPVVFGGGTKLTVLGQPKGAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (Z), FASTA

>6Q0O_3 H2227 Fab heavy chain (chains Z)
QVQLQESGPGLVKPSGTLSLTCAVSGGSISSSQWWSWVRQPPGKGLEWIGEISHGVYTNY
NPSLKSRVTISADKSQNQFSLNLSSVTAADTAVYYCARAPPYCSSASCPDDYYYFFLDVW
GKGTTVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (TRS, GOL, 1PE) are not listed.

Primary citation

Affinity maturation in a human humoral response to influenza hemagglutinin. McCarthy, K.R., Raymond, D.D., Do, K.T. et al. Proc Natl Acad Sci U S A (2019). DOI 10.1073/pnas.1915620116 · PubMed

Other PDB entries of the same protein (UniProt A7UPX0), best resolution first:

5W0D 1.9 Å, Inferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza…
4HKX 2.5 Å, Influenza hemagglutinin in complex with CH67 Fab
4YJZ 2.72 Å, Human antibody H2526 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
5W6G 2.79 Å, Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
4YK4 2.8 Å, Human antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
9E6J 2.98 Å, DH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islands/3/2006
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
6WIZ 4.2 Å, Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin
5UJZ 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK0 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK1 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK2 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…

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