6A0Z: Broadly neutralizing antibody 13D4

Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza hemagglutinin, HA head region. Determined by X-ray diffraction at 2.33 Å resolution. Released 20 Jun 2018.

Method: X-ray diffraction
Resolution: 2.33 Å
Organisms: Influenza A virus, Human immunodeficiency virus 1, Mus musculus
Chains: 3
Atoms: 5,804
Mol. weight: 110.87 kDa
Ligands: NAG
Released: 20 Jun 2018

Explore 6A0Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6A0Z contains 23 α-helices and 72 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: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	51-54	4	1
β-strand	56	1	1
β-strand	59-60	2	2
β-strand	64	1	3
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	2
β-strand	95	1	3
β-strand	100-102	3	4
α-helix	105-112	8
β-strand	117-122	6	4
α-helix	125a-126	3
β-strand	131	1	5
β-strand	136-141	6	6
β-strand	144-146	3	6
β-strand	151-153	3	4
β-strand	155	1	5
β-strand	157	1	7
β-strand	160	1	7
α-helix	162-163	2
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	7	4
β-strand	267-269	3	2
β-strand	274-279	6	1
β-strand	281-283	3	10
β-strand	286-288	3	10
β-strand	302	1	10

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	46-52	7	12
β-strand	56-59	4	12
α-helix	61-63	3
β-strand	67-72	6	11
β-strand	74-79	6	11
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	100f-103	4	12
β-strand	107-111	5	12
α-helix	115-116	2
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-124	5	14
α-helix	125-127	3
β-strand	135-145	11	14
β-strand	146	1	13
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-171	3	14
β-strand	174-184	11	14
β-strand	194-199	6	15
β-strand	204-209	6	15

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	16
β-strand	10-13	4	12
β-strand	19-25	7	16
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-106	5	12
β-strand	111	1	17
α-helix	112-113	2
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	124-127	4
β-strand	129-139	11	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	153-155	3	19
β-strand	159-163	5	18
α-helix	164-167	4
β-strand	173-182	10	18
α-helix	183-186	4
β-strand	191-197	7	19
α-helix	204	1
β-strand	205-210	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin,Envelope glycoprotein	A	protein	551	Influenza A virus, Human immunodeficiency virus 1	M1E1E4 (AlphaFold model), Q6DQ34
Antibody 13D4, Fab Heavy Chain	H	protein	224	Mus musculus
Antibody 13D4, Fab Light Chain	L	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>6A0Z_1 Hemagglutinin,Envelope glycoprotein (chains A)
MDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLDGVKPLILRDCSVAG
WLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPK
SSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIH
HPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAI
NFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTI
GECPKYVKSNRLVLATGLRNSPQRERRRKKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNE
QGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFL
DVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECM
ESVRNGTYDYPQYSEEARLKREEISSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLL
STFLGHHHHHH

Sequence of entity 2 (H), FASTA

>6A0Z_2 Antibody 13D4, Fab Heavy Chain (chains H)
QVQLQQSGAELMKPGASVKISCKATGYTFSGHWIEWVKQRPGHGLEWIGEILPGSGNIHY
NEKFKGKATFAADTSSNTAYMQLSSLTSEDSAVYYCARLGTTAVERDWYFDVWGAGTTVT
VSLADPSAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL
QSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG

Sequence of entity 3 (L), FASTA

>6A0Z_3 Antibody 13D4, Fab Light Chain (chains L)
DIVMTQSQKFMSASVGDRVSVTCKASQNVGTHLAWYQQKPGQSPKALIYSASYRYSGVPD
RFTGSGSGTDFTLTISNVQSGDLADYFCQQYNNFPLTFGAGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTRDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

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

Primary citation

Structural Basis for the Broad, Antibody-Mediated Neutralization of H5N1 Influenza Virus. Lin, Q., Li, T., Chen, Y. et al. J Virol (2018) 92. DOI 10.1128/JVI.00547-18 · PubMed

Other PDB entries of the same protein (UniProt M1E1E4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BJM 2.07 Å, Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein
6VKE 2.1 Å, Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein
5KWW 2.5 Å, Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein
6VKD 2.5 Å, Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein
6VKC 2.6 Å, Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein
7ZRV 2.8 Å, cryo-EM structure of omicron spike in complex with de novo designed binder, full map
7AD1 2.92 Å, Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G,…
7QTI 3.04 Å, SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)
5U68 3.08 Å, Structural basis for antibody cross-neutralization of respiratory syncytial virus and…
6W16 3.1 Å, Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458…
7FJN 3.25 Å, Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex…
6OUS 3.4 Å, Structure of fusion glycoprotein from human respiratory syncytial virus

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