7JIX: Hemagglutinin HA1 chain

Murine antibody that engages the influenza hemagglutinin receptor binding site. Determined by X-ray diffraction at 3.9 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 3.9 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006 (Egg passage)(H1N1)), Influenza A virus (A/Mexico/UASLP-006/2008(H1N1)), Mus musculus
Chains: 4
Atoms: 7,365
Mol. weight: 107.9 kDa
Released: 28 Jul 2021

Explore 7JIX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JIX contains 28 α-helices and 101 β-strands across 4 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: 8 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	9-11	3	2
β-strand	12	1	3
β-strand	19-20	2	4
β-strand	28-29	2	4
β-strand	30	1	5
β-strand	33-35	3	6
β-strand	37-38	2	7
β-strand	45	1	8
β-strand	48	1	9
β-strand	51	1	9
β-strand	54-57	4	10
β-strand	59	1	11
α-helix	61-65	5
α-helix	69-74	6
β-strand	79	1	12
β-strand	83-85	3	10
β-strand	91	1	11
β-strand	99	1	13
α-helix	102-111	10
β-strand	112-114	3	12
β-strand	117-119	3	13
α-helix	123-126	4
β-strand	131	1	14
β-strand	136-140	5	15
β-strand	145-146	2	15
β-strand	151-153	3	13
β-strand	155	1	14
β-strand	157	1	16
β-strand	160	1	16
β-strand	164	1	17
β-strand	167-169	3	17
β-strand	176-184	9	13
α-helix	188-194	7
β-strand	202-206	5	17
β-strand	209-213	5	17
β-strand	223	1	18
β-strand	226	1	18
β-strand	229-237	9	13
α-helix	238	1
β-strand	242-247	6	17
β-strand	251-254	4	13
β-strand	256-259	4	13
β-strand	261-262	2	12
β-strand	268-270	3	10
α-helix	273-274	2
β-strand	275	1	8
β-strand	283-284	2	19
β-strand	287-288	2	19
β-strand	295-296	2	7
β-strand	303	1	19
β-strand	306	1	20
α-helix	307	1
β-strand	308-309	2	7
β-strand	316-318	3	6
β-strand	322	1	5

Chain B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	506	1	21
β-strand	510	1	21
β-strand	514	1	3
β-strand	522-524	3	2
β-strand	535-536	2	2
α-helix	538-557	20
α-helix	560-561	2
β-strand	562	1	20
α-helix	575-625	51
β-strand	630-632	3	1
β-strand	637-640	4	1
α-helix	646-649	4
α-helix	659-670	12

Chain H: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	29
β-strand	11-12	2	30
β-strand	18-25	8	29
α-helix	29-31	3
β-strand	34-39	6	24
α-helix	44	1
β-strand	45-52	8	24
β-strand	57-60	4	24
α-helix	62-64	3
β-strand	68-73	6	29
β-strand	78-83	6	29
β-strand	92-98	7	24
β-strand	105-106	2	24
β-strand	110-112	3	24
β-strand	113-114	2	30
α-helix	121-122	2
β-strand	123-127	5	31
β-strand	138-148	11	31
β-strand	154-157	4	32
β-strand	167-168	2	31
α-helix	169-171	3
β-strand	172-174	3	31
β-strand	177-187	11	31
α-helix	188-190	3
β-strand	197-202	6	32
β-strand	207-212	6	32

Chain L: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	22
β-strand	6-7	2	23
β-strand	10-14	5	24
β-strand	19-24	6	23
β-strand	31	1	25
β-strand	34	1	25
β-strand	37-42	6	24
α-helix	47-48	2
β-strand	49-53	5	24
β-strand	57-58	2	24
α-helix	59	1
β-strand	66-71	6	23
β-strand	74-79	6	23
α-helix	84-86	3
β-strand	89-94	6	24
α-helix	100	1
β-strand	101-102	2	24
β-strand	103	1	22
β-strand	106-111	6	24
β-strand	115	1	26
β-strand	118-122	5	27
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	27
β-strand	144	1	26
β-strand	149-154	6	28
β-strand	157-159	3	28
β-strand	163-168	6	27
α-helix	169-171	3
β-strand	177-186	10	27
α-helix	187-190	4
β-strand	196-201	6	28
α-helix	208	1
β-strand	209-213	5	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A	protein	334	Influenza A virus (A/Solomon Islands/3/2006 (Egg passage)(H1N1))	A7Y8A6
Hemagglutinin HA2 chain	B	protein	177	Influenza A virus (A/Mexico/UASLP-006/2008(H1N1))	G2TTT7
Fab light chain	L	protein	220	Mus musculus
Fab heavy chain	H	protein	227	Mus musculus

Sequence of entity 1 (A), FASTA

>7JIX_1 Hemagglutinin HA1 chain (chains A)
ADPGYLLEDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQL
GNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFE
RFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEV
LVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTL
LEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQ
NVHPVTIGECPKYVRSAKLRMVTGLRNIPSIQSR

Sequence of entity 2 (B), FASTA

>7JIX_2 Hemagglutinin HA2 chain (chains B)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKIDGVR

Sequence of entity 3 (L), FASTA

>7JIX_3 Fab light chain (chains L)
ASDIVLTQSPASLAVSLGQRATISCKASQSVDFDGDSYMNWYQQKPGQPPKLLIYTTSNL
ESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQSSEDPYTFGGGTKLEIKRADGAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 4 (H), FASTA

>7JIX_4 Fab heavy chain (chains H)
ASEVQLQESGPELVKPGASVKISCKASGYAFSRSWMNWVKQRPGKGLEWIGRIYPGDGDT
NYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCARGSNSFAYWGQGTLVTVSGAK
TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGHHHHHH

Primary citation

Murine antibody that engages the influenza hemagglutinin receptor binding site. Bajic, G., Schmidt, A.G. To be published.

Other PDB entries of the same protein (UniProt A7Y8A6), best resolution first:

5UGY 2.8 Å, Influenza hemagglutinin in complex with a neutralizing antibody

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