6E4X: Human antibody S5V2-29

Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2). Determined by X-ray diffraction at 2.25 Å resolution. Released 22 May 2019.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Influenza A virus (A/Texas/50/2012(H3N2)), Homo sapiens
Chains: 3
Atoms: 5,835
Mol. weight: 84.21 kDa
Ligands: NAG
Released: 22 May 2019

Explore 6E4X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E4X contains 21 α-helices and 76 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 B: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	38-40	3
β-strand	43-44	2	1
β-strand	51-54	4	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
α-helix	105-115	11
β-strand	117	1	4
β-strand	120-122	3	5
β-strand	130-131	2	6
β-strand	136-140	5	7
β-strand	145-146	2	7
β-strand	151-153	3	5
β-strand	155-156	2	6
β-strand	157	1	8
β-strand	160	1	8
β-strand	164-168	5	9
β-strand	175-184	10	5
α-helix	188-195	8
β-strand	202-205	4	9
β-strand	210-213	4	9
β-strand	223	1	10
β-strand	226	1	10
β-strand	229-237	9	5
β-strand	243-247	5	9
β-strand	251-254	4	5
β-strand	256-260	5	5
β-strand	266-269	4	3
α-helix	272-273	2
β-strand	274-278	5	2
β-strand	281-283	3	11
β-strand	286-288	3	11
β-strand	294-295	2	1
β-strand	302-303	2	11
α-helix	306	1
β-strand	307-308	2	1

Chain Y: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	34-38	5	13
β-strand	45-49	5	13
β-strand	53-54	2	13
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
β-strand	93-94	2	13
β-strand	98-103	6	13
β-strand	107	1	14
α-helix	108-109	2
β-strand	110-114	5	15
α-helix	115-117	3
α-helix	118-122	5
β-strand	125-135	11	15
β-strand	136	1	14
β-strand	141-146	6	16
β-strand	149-150	2	16
β-strand	155-159	5	15
α-helix	160-163	4
β-strand	169-178	10	15
α-helix	179-183	5
β-strand	188-193	6	16
β-strand	201-205	5	16

Chain Z: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
β-strand	35-42	8	19
β-strand	46-53	8	19
β-strand	59-61	3	19
β-strand	69-74	6	17
β-strand	79-84	6	17
α-helix	89-91	3
β-strand	93-106	14	19
β-strand	111-120	10	19
β-strand	124-126	3	19
β-strand	127-128	2	18
α-helix	132-133	2
β-strand	134	1	20
α-helix	135-136	2
β-strand	137-141	5	21
α-helix	145-147	3
β-strand	148	1	21
β-strand	152-162	11	21
β-strand	163	1	20
β-strand	168-171	4	22
α-helix	172-174	3
β-strand	180-182	3	21
α-helix	183-185	3
β-strand	186-187	2	21
β-strand	193-202	10	21
α-helix	203-206	4
β-strand	211-217	7	22
α-helix	218-220	3
β-strand	222-228	7	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	B	protein	291	Influenza A virus (A/Texas/50/2012(H3N2))	R4L1D1
S5V2-29 light chain	Y	protein	210	Homo sapiens	Q8TCD0 (AlphaFold model)
S5V2-29 heavy chain	Z	protein	241	Homo sapiens

Sequence of entity 1 (B), FASTA

>6E4X_1 Hemagglutinin (chains B)
TNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSN
CYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTH
LNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPN
IGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGK
CKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGGALEVLFQ

Sequence of entity 2 (Y), FASTA

>6E4X_2 S5V2-29 light chain (chains Y)
DIQMTQTPSSLSASVGDRVTITCRASQSIGASLNWYQQKPGEAPKFLIYAASNLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQQGTFGQGTKLEIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKA
DYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (Z), FASTA

>6E4X_3 S5V2-29 heavy chain (chains Z)
QVQLQESGPGLVKPSETLSLTCTVSGGSVSSNIYYWSWIRQTPGKGLEWLGYFYHSGSSN
YNPSLKSRVTISGDMSKNQFSLKLKSVTAADTAIYYCARGGVENLMLVAVIQEMWYFDLW
GRGTLVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (GOL) 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 R4L1D1), best resolution first:

5W08 2.6 Å, A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab
6XQ2 3.0 Å, Human antibody S8V2-37 in complex with the influenza hemagglutinin head domain of…
6XPY 3.6 Å, Human antibody S1V2-58 in complex with the influenza hemagglutinin head domain of…
6XPR 4.09 Å, Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain…
6XPQ 4.2 Å, Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of…

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