6XSK: Vaccine-Elicited Rhesus Antibody 789-203-3C12

Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with Stabilized SI06 (A/Solomon Islands/3/06) Influenza Hemagglutinin Trimer. Determined by electron microscopy at 3.85 Å resolution. Released 21 Jul 2021.

Method: Electron microscopy
Resolution: 3.85 Å
Organisms: Macaca mulatta, Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Chains: 12
Atoms: 17,322
Mol. weight: 415.75 kDa
Ligands: NAG
Released: 21 Jul 2021

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

Secondary structure: helices and β-sheets

6XSK contains 48 α-helices and 211 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, 38 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	8
β-strand	18	1	9
β-strand	24-26	3	10
β-strand	34-36	3	10
β-strand	39-41	3	11
β-strand	43-44	2	12
β-strand	51-53	3	13
β-strand	54	1	14
β-strand	56	1	14
α-helix	57-58	2
β-strand	59	1	15
α-helix	66-70	5
α-helix	74-81	8
β-strand	84	1	16
β-strand	87	1	15
β-strand	102	1	17
α-helix	105-111	7
β-strand	115	1	16
β-strand	118-121	4	17
β-strand	130	1	18
β-strand	136-141	6	19
β-strand	144-146	3	19
β-strand	151-153	3	17
β-strand	156	1	18
β-strand	157	1	20
β-strand	160	1	20
β-strand	164-169	6	21
β-strand	175-183	9	17
α-helix	188-195	8
β-strand	202-205	4	21
β-strand	210-213	4	21
β-strand	230-237	8	17
β-strand	242-247	6	21
β-strand	251-254	4	17
β-strand	257-260	4	17
α-helix	272-273	2
β-strand	274-278	5	13
β-strand	281-282	2	22
β-strand	287-288	2	22
β-strand	294-295	2	12
β-strand	302-303	2	22
α-helix	306	1
β-strand	307-308	2	12
β-strand	315-317	3	11
β-strand	321	1	10

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	9
β-strand	22-27	6	8
β-strand	32-34	3	8
α-helix	38-57	20
β-strand	64-65	2	22
α-helix	75-125	51
β-strand	130-132	3	8
β-strand	137-140	4	8
α-helix	146-154	9
α-helix	163-172	10

Chain C: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	23
β-strand	18	1	24
β-strand	25-28	4	25
β-strand	31-35	5	25
β-strand	36	1	26
β-strand	39-41	3	27
β-strand	43-44	2	28
β-strand	51-54	4	29
β-strand	56	1	29
α-helix	57-58	2
β-strand	59-60	2	30
α-helix	66-70	5
α-helix	76-81	6
β-strand	87-89	3	30
β-strand	102	1	31
α-helix	105-112	8
β-strand	118-122	5	31
β-strand	131	1	32
β-strand	136-141	6	33
β-strand	144-146	3	33
β-strand	151-153	3	31
β-strand	155	1	32
β-strand	157	1	34
β-strand	160	1	34
β-strand	164-169	6	35
β-strand	175-184	10	31
α-helix	188-195	8
β-strand	202-205	4	35
β-strand	210-213	4	35
β-strand	229-237	9	31
α-helix	238	1
β-strand	242-247	6	35
β-strand	251-254	4	31
β-strand	256-260	5	31
β-strand	268-269	2	30
α-helix	272-273	2
β-strand	274-279	6	29
β-strand	281-282	2	36
β-strand	294-295	2	28
β-strand	302-303	2	36
α-helix	306	1
β-strand	307-308	2	28
β-strand	315-317	3	27
β-strand	321	1	26

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	24
β-strand	22-27	6	23
β-strand	33-34	2	23
α-helix	38-58	21
β-strand	65	1	36
α-helix	72-74	3
α-helix	75-126	52
β-strand	130-132	3	23
β-strand	137-140	4	23
α-helix	146-154	9
α-helix	163-172	10

Chain E: 7 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	37
β-strand	18	1	38
β-strand	25-26	2	39
β-strand	34-35	2	39
β-strand	36	1	40
β-strand	39-41	3	41
β-strand	43-44	2	42
β-strand	51-54	4	43
β-strand	56	1	43
α-helix	57-58	2
β-strand	59-60	2	44
β-strand	64	1	45
α-helix	66-71	6
α-helix	74-78	5
β-strand	84	1	46
β-strand	87-89	3	44
β-strand	95	1	45
β-strand	102	1	46
α-helix	105-111	7
β-strand	115-122	8	46
β-strand	130	1	47
β-strand	136-141	6	48
β-strand	144-146	3	48
β-strand	151-153	3	46
β-strand	156	1	47
β-strand	157	1	49
β-strand	160	1	49
β-strand	164-169	6	50
β-strand	175-184	10	46
α-helix	188-195	8
β-strand	202-205	4	50
β-strand	210-213	4	50
β-strand	229-237	9	46
β-strand	242-247	6	50
β-strand	251-254	4	46
β-strand	256-262	7	46
β-strand	267-269	3	44
α-helix	272-273	2
β-strand	274-279	6	43
β-strand	281	1	51
β-strand	282	1	52
β-strand	288	1	51
β-strand	294-295	2	42
β-strand	302	1	52
α-helix	306	1
β-strand	307-308	2	42
β-strand	315-317	3	41
β-strand	321	1	40

Chain F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	38
β-strand	22-27	6	37
β-strand	32-33	2	37
α-helix	38-57	20
β-strand	65	1	52
α-helix	72-74	3
α-helix	75-125	51
β-strand	130-132	3	37
β-strand	137-140	4	37
α-helix	146-154	9
α-helix	163-172	10

Chain G: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	56
β-strand	11-12	2	57
β-strand	18-25	8	56
β-strand	34-39	6	23
β-strand	46-52	7	23
β-strand	56-59	4	23
α-helix	64-66	3
β-strand	67-70	4	56
α-helix	73-75	3
β-strand	77-82	6	56
α-helix	84-86	3
β-strand	88-95	8	23
β-strand	98-99	2	58
β-strand	100B-100C	2	58
α-helix	100D	1
β-strand	100H-103	4	23
β-strand	107-109	3	23
β-strand	110-111	2	57

Chain H: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	18-25	8	4
β-strand	33-39	7	6
β-strand	46-51	6	6
β-strand	59	1	6
α-helix	61-63	3
β-strand	68-72	5	4
β-strand	77-82	6	4
α-helix	84-86	3
β-strand	88-95	8	6
β-strand	98-99	2	7
β-strand	100B-100C	2	7
α-helix	100D	1
β-strand	102-103	2	6
β-strand	107-109	3	6
β-strand	110-111	2	5

4 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
789-203-3C12 Fab Light Chain	J, K, L	protein	214	Macaca mulatta
789-203-3C12 Fab Heavy Chain	G, H, I	protein	455	Macaca mulatta
Hemagglutinin HA1 chain	A, C, E	protein	343	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8I1
Hemagglutinin HA2 chain	B, D, F	protein	222	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7Y8I1

Sequence of entity 1 (J, K, L), FASTA

>6XSK_1 789-203-3C12 Fab Light Chain (chains J, K, L)
DIQMTQSPSSLSASVGDTVTITCRASQSISSWLAWYQQKPGKAPNLLIYRASTLQSGVPS
RFSGSGSGTDFTLTISSLQSEDFATYFCQQSTSSPFTFGPGTKLDIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (G, H, I), FASTA

>6XSK_2 789-203-3C12 Fab Heavy Chain (chains G, H, I)
QVQLQESGPGLVKPSEILSLTCAVSGGSFSSYCWGWIRQPPGKGLEWIGSICGSGGSNYL
NPSLKSRVTLSVDTSKNQFSLILNSVTAADTAVYYCAREGITIFGVVIPRVLDSWGQGAV
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAP
ELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPR
EEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLP
PSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTV
DKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Sequence of entity 3 (A, C, E), FASTA

>6XSK_3 Hemagglutinin HA1 chain (chains A, C, E)
MKVKLLVLLCTFTATYADTICIGYHANNSTDTVDTVCEKNVTVTHSVNLLEDSHNGKLCL
LKGIAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELRE
QLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKS
YANNKEKEVLVLWGVHHPPNIGDQRALYHKENAYVSVVSSHYSRKFTPEIAKRPKVRDQE
GRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQG
AINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLRNIPSIQSR

Sequence of entity 4 (B, D, F), FASTA

>6XSK_4 Hemagglutinin HA2 chain (chains B, D, F)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINCITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKIDGVSGRL
VPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

Primary citation

Co-immunization with hemagglutinin stem immunogens elicits cross-group neutralizing antibodies and broad protection against influenza A viruses. Moin, S.M., Boyington, J.C., Boyoglu-Barnum, S. et al. Immunity (2022) 55:2405-2418.e7. DOI 10.1016/j.immuni.2022.10.015 · PubMed

Other PDB entries of the same protein (UniProt A7Y8I1), best resolution first:

6CF7 2.72 Å, Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin in…
6FYT 2.8 Å, Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38
5UGY 2.8 Å, Influenza hemagglutinin in complex with a neutralizing antibody
9CU7 2.82 Å, Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus…
6OC3 2.85 Å, Crystal structure of FluA-20 Fab in complex with the head domain of H1 (A/Solomon…
9DBX 2.9 Å, Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza…
7UMM 3.36 Å, H1 Solomon Islands 2006 hemagglutinin in complex with Ab109
8U44 3.41 Å, CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06
7UMN 3.6 Å, H1 Solomon Islands 2006 hemagglutinin in complex with Ab36
6WIZ 4.2 Å, Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin

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