4XNM: Antibody Influenza H5 Complex

Antibody Influenza H5 Complex. Determined by X-ray diffraction at 2.51 Å resolution. Released 15 Jul 2015.

Method: X-ray diffraction
Resolution: 2.51 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 6
Atoms: 9,769
Mol. weight: 145.86 kDa
Released: 15 Jul 2015

Explore 4XNM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XNM contains 38 α-helices and 140 β-strands across 6 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.

Chains A and L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	14
β-strand	8-11	4	15
β-strand	17-22	6	14
α-helix	26-28	3
β-strand	32-36	5	15
β-strand	43-46	4	15
β-strand	47	1	16
β-strand	51	1	16
β-strand	60-65	6	14
β-strand	68-73	6	14
α-helix	78-80	3
β-strand	82-90	9	15
β-strand	93-96	4	15
β-strand	100-104	5	15
β-strand	110	1	17
α-helix	111-112	2
β-strand	113-117	5	18
α-helix	118-120	3
α-helix	121-125	5
β-strand	129-138	10	18
β-strand	139	1	17
β-strand	144-149	6	19
β-strand	152-154	3	19
β-strand	158-160	3	18
α-helix	161-163	3
β-strand	164-165	2	18
β-strand	171-179	9	18
α-helix	181-186	6
β-strand	190-196	7	19
β-strand	199-205	7	19

Chain B: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	11-12	2	21
β-strand	18-25	8	20
β-strand	34-40	7	22
β-strand	47-52	6	22
β-strand	58-60	3	22
β-strand	68-73	6	20
β-strand	78-83	6	20
α-helix	88-90	3
β-strand	92-101	10	22
β-strand	104	1	23
β-strand	108-113	6	22
α-helix	114	1
β-strand	117-119	3	22
β-strand	120-121	2	21
β-strand	127	1	24
α-helix	128-129	2
β-strand	130-134	5	25
β-strand	146-155	10	25
β-strand	156	1	24
β-strand	161-164	4	26
α-helix	165-167	3
β-strand	169	1	26
β-strand	173-175	3	25
α-helix	176-178	3
β-strand	179-180	2	25
β-strand	186-194	9	25
α-helix	196-198	3
β-strand	204-210	7	26
α-helix	211-213	3
β-strand	215-221	7	26

Chain C: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	64	1	27
α-helix	66-71	6
β-strand	95	1	27
β-strand	100-102	3	28
α-helix	105-111	7
β-strand	117-122	6	28
α-helix	125A-126	3
β-strand	131	1	29
β-strand	136-141	6	10
β-strand	144-146	3	10
β-strand	151-153	3	28
β-strand	155	1	29
β-strand	157	1	30
β-strand	160	1	30
α-helix	162-163	2
β-strand	164-169	6	31
β-strand	175-184	10	28
α-helix	188-195	8
β-strand	202-205	4	31
β-strand	210-213	4	31
β-strand	223	1	32
β-strand	226	1	32
β-strand	229-237	9	28
β-strand	242-247	6	31
β-strand	251-254	4	28
β-strand	256-261	6	28

Chain D: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	59-60	2	33
β-strand	64	1	34
α-helix	66-71	6
β-strand	78	1	31
β-strand	84	1	35
β-strand	87-88	2	33
β-strand	95	1	34
β-strand	100-102	3	35
α-helix	105-111	7
β-strand	118-122	5	35
α-helix	125A-126	3
β-strand	131	1	36
β-strand	136-141	6	23
β-strand	144-146	3	23
β-strand	151-153	3	35
β-strand	155	1	36
β-strand	157	1	37
β-strand	160	1	37
α-helix	162-163	2
β-strand	164-169	6	38
β-strand	175-184	10	35
α-helix	188-195	8
β-strand	202-205	4	38
β-strand	210-213	4	38
β-strand	223	1	39
β-strand	226	1	39
β-strand	229-237	9	35
β-strand	242-247	6	38
β-strand	251-254	4	35
β-strand	256-260	5	35

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	34-40	7	9
β-strand	47-52	6	9
β-strand	58-60	3	9
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-101	10	9
β-strand	104	1	10
β-strand	108-113	6	9
α-helix	114	1
β-strand	117-119	3	9
β-strand	120-121	2	8
β-strand	127	1	11
α-helix	128-129	2
β-strand	130-134	5	12
β-strand	145-155	11	12
β-strand	156	1	11
β-strand	161-164	4	13
α-helix	165-167	3
β-strand	169	1	13
β-strand	173-175	3	12
α-helix	176-178	3
β-strand	179-180	2	12
β-strand	186-195	10	12
α-helix	196-198	3
β-strand	205-210	6	13
α-helix	211-213	3
β-strand	215-220	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H5.3 FAB Light Chain	A, L	protein	208	Homo sapiens
H5.3 FAB Heavy Chain	B, H	protein	227	Homo sapiens
Hemagglutinin	C, D	protein	231	Influenza A virus	Q6DQ33

Sequence of entity 1 (A, L), FASTA

>4XNM_1 H5.3 FAB Light Chain (chains A, L)
YELTQPPSVSVSPGQTVNITCSGDTLGDKYVCWYQQKPGQSPVLVIYQDTKRPSGIPERF
SGSNSGDTATLTVSGTQAMDEADYYCQAWDSSSFVFGTGTKVTVLGQPKANPTVTLFPPS
SEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLT
PEQWKSHRSYSCQVTHEGSTVEKTVAPT

Sequence of entity 2 (B, H), FASTA

>4XNM_2 H5.3 FAB Heavy Chain (chains B, H)
QVQLQESGPGLVKPSGTVSLTCAVSGGSISSSYWWSWVRQPPGKGLEWIGEIYHSGNTNY
NPSLKSRVTISVDKSKNLFSLKLSSVTAADTAVYYCARVALFDILTGGWFDPWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVELKTPT

Sequence of entity 3 (C, D), FASTA

>4XNM_3 Hemagglutinin (chains C, D)
MGSSHHHHHHSSGLVPRGSKPLILRDCSVAGWLLGNPMCDEFINVPEWSYIVEKANPVND
LCYPGDFNDYEELKHLLSRINHFEKIQIIPKSSWSSHEASLGVSSACPYQGKSSFFRNVV
WLIKKNSTYPTIKRSYNNTNQEDLLVLWGIHHPNDAAEQTKLYQNPTTYISVGTSTLNQR
LVPRIATRSKVNGQSGRMEFFWTILKPNDAINFESNGNFIAPEYAYKIVKK

Primary citation

Vaccine-elicited antibody that neutralizes H5N1 influenza and variants binds the receptor site and polymorphic sites. Winarski, K.L., Thornburg, N.J., Yu, Y. et al. Proc Natl Acad Sci U S A (2015) 112:9346-9351. DOI 10.1073/pnas.1502762112 · PubMed

Other PDB entries of the same protein (UniProt Q6DQ33), best resolution first:

4FQI 1.71 Å, Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza virus hemagglutinin
4XNQ 2.0 Å, Antibody hemagglutinin Complexes
6CF5 2.04 Å, Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in…
4KDO 2.4 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDN 2.48 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDM 2.5 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus
3GBM 2.7 Å, Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.
4XRC 2.74 Å, Antibody hemagglutinin Complexes
5A3I 2.89 Å, Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5…
6E3H 2.9 Å, Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin
4N5Z 2.95 Å, Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D,…
6E7G 3.09 Å, Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1…

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