5UMN: C05 VPGSGW mutant

Crystal structure of C05 VPGSGW mutant bound to H3 influenza hemagglutinin, HA1 subunit. Determined by X-ray diffraction at 1.97 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 1.97 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 6
Atoms: 12,093
Mol. weight: 162.36 kDa
Ligands: FLC, NAG
Released: 24 May 2017

Explore 5UMN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UMN contains 51 α-helices and 152 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.

Chain A: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	44	1	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	130-134	5	5
β-strand	135	1	6
β-strand	136-141	6	7
β-strand	144-146	3	7
β-strand	151-156	6	5
β-strand	157	1	8
β-strand	160	1	8
β-strand	164-169	6	9
β-strand	176-184	9	5
α-helix	188-195	8
β-strand	201-205	5	9
β-strand	210-213	4	9
α-helix	219-222	4
β-strand	223	1	10
β-strand	226	1	10
β-strand	229-237	9	5
β-strand	242-249	8	9
β-strand	251-254	4	5
β-strand	256-259	4	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	1	11
α-helix	306	1
β-strand	307-308	2	1

Chain B: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	52	1	12
β-strand	58-60	3	13
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	14
β-strand	86-89	4	13
β-strand	100-101	2	15
α-helix	105-115	11
β-strand	117	1	14
β-strand	120-122	3	15
β-strand	130-134	5	15
β-strand	135	1	16
β-strand	136-141	6	17
β-strand	144-146	3	17
β-strand	151-156	6	15
β-strand	157	1	18
β-strand	160	1	18
β-strand	164-169	6	19
β-strand	176-184	9	15
α-helix	188-195	8
β-strand	201-205	5	19
β-strand	210-213	4	19
α-helix	220-222	3
β-strand	223	1	20
β-strand	226	1	20
β-strand	229-237	9	15
β-strand	242-249	8	19
β-strand	251-254	4	15
β-strand	256-259	4	15
α-helix	260	1
β-strand	266-269	4	13
β-strand	275	1	12

Chain C: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	27B-27D	3
α-helix	29-31	3
β-strand	32-39	8	22
β-strand	45-51	7	22
β-strand	58-59	2	22
β-strand	67-72	6	21
α-helix	73-75	3
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-98	11	22
β-strand	100-100A	2	16
β-strand	100F-100G	2	16
β-strand	100P-103	4	22
β-strand	107-111	5	22
β-strand	117	1	23
α-helix	118-119	2
β-strand	120-124	5	24
β-strand	132	1	24
β-strand	135-145	11	24
β-strand	146	1	23
β-strand	151-154	4	25
α-helix	155-157	3
β-strand	159	1	25
β-strand	163-165	3	24
α-helix	166-168	3
β-strand	169-170	2	24
β-strand	176-185	10	24
α-helix	186-188	3
β-strand	195-200	6	25
α-helix	201-203	3
β-strand	205-210	6	25

Chain D: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-14	5	27
β-strand	19-25	7	26
β-strand	33-38	6	27
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-67	6	26
β-strand	70-75	6	26
α-helix	80-82	3
β-strand	84-90	7	27
α-helix	96	1
β-strand	97-98	2	27
β-strand	102-107	6	27
β-strand	111	1	28
α-helix	112-113	2
β-strand	114-118	5	29
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	145-150	6	30
β-strand	153-154	2	30
α-helix	155	1
β-strand	159-163	5	29
α-helix	164-167	4
β-strand	173-182	10	29
α-helix	183-187	5
β-strand	191-197	7	30
β-strand	205-210	6	30

Chain E: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	11-12	2	32
β-strand	18-25	8	31
β-strand	27A	1	33
β-strand	27E	1	33
α-helix	29-31	3
β-strand	32-39	8	34
β-strand	45-51	7	34
β-strand	58-59	2	34
β-strand	67-72	6	31
α-helix	73-75	3
β-strand	77-82	6	31
α-helix	84-86	3
β-strand	88-98	11	34
β-strand	100-100A	2	6
β-strand	100F-100G	2	6
β-strand	100P-103	4	34
β-strand	107-109	3	34
β-strand	110-111	2	32
α-helix	115-116	2
β-strand	117	1	35
α-helix	118-119	2
β-strand	120-124	5	36
α-helix	125-127	3
α-helix	132-134	3
β-strand	135-145	11	36
β-strand	146	1	35
β-strand	151-154	4	37
α-helix	155-157	3
β-strand	159	1	37
β-strand	164-165	2	36
α-helix	166-168	3
β-strand	169-170	2	36
β-strand	176-185	10	36
α-helix	186-188	3
β-strand	195-200	6	37
α-helix	201-203	3
β-strand	205-210	6	37

Chain F: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	38
β-strand	10-13	4	39
β-strand	19-25	7	38
β-strand	33-38	6	39
β-strand	44-49	6	39
β-strand	53-54	2	39
α-helix	55	1
β-strand	62-67	6	38
β-strand	70-75	6	38
α-helix	80-82	3
β-strand	84-90	7	39
α-helix	96	1
β-strand	97-98	2	39
β-strand	102-106	5	39
β-strand	111	1	40
α-helix	112-113	2
β-strand	114-118	5	41
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	41
β-strand	140	1	40
β-strand	145-150	6	42
β-strand	153-154	2	42
α-helix	155	1
β-strand	159-163	5	41
α-helix	164-167	4
β-strand	173-182	10	41
α-helix	183-187	5
β-strand	191-197	7	42
β-strand	205-210	6	42

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, B	protein	274	Influenza A virus	Q91MA7
Antibody C05 VPGSGW mutant, heavy chain	C, E	protein	247	Homo sapiens
Antibody C05, light chain	D, F	protein	214	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>5UMN_1 Hemagglutinin (chains A, B)
VQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDV
PDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYP
VLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPW
VRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECI
TPNGSIPNDKPFQNVNKITYGACPKYVGHHHHHH

Sequence of entity 2 (C, E), FASTA

>5UMN_2 Antibody C05 VPGSGW mutant, heavy chain (chains C, E)
QVQLQESGGGLVQPGESLRLSCVGSGSSFGESTLSYYAVSWVRQAPGKGLEWLSIINAGG
GDIDYADSVEGRFTISRDNSKETLYLQMTNLRVEDTGVYYCAKHMSMQQVPGSGWERADL
VGDAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWN
SGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS
CHHHHHH

Sequence of entity 3 (D, F), FASTA

>5UMN_3 Antibody C05, light chain (chains D, F)
DIQLTQSPSSLSASVGDRVTLTCQASQDIRKFLNWYQQKPGKGPKLLIYDASNLQRGVPS
RFSGGGSGTDFTLIISSLQPEDVGTYYCQQYDGLPFTFGGGTKVVIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (NA, 1PE) are not listed.

Primary citation

In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity. Wu, N.C., Grande, G., Turner, H.L. et al. Nat Commun (2017) 8:15371-15371. DOI 10.1038/ncomms15371 · PubMed

Other PDB entries of the same protein (UniProt Q91MA7), best resolution first:

4FNK 1.9 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin
8IB1 1.95 Å, Structure of the LAH31 Fab bound to an influenza virus HA epitope peptide
6NHR 2.1 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2…
6OCB 2.1 Å, Crystal structure of FluA-20 Fab in complex with the head domain of H3 (A/Hong…
5VTZ 2.15 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
7QA4 2.19 Å, Crystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglutinin at 2.2 Angstrom
6BKM 2.2 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D…
6TZB 2.24 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin in…
5VTV 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
5VU4 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin…
6BKQ 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin E190D…
6NHP 2.25 Å, Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin HA2…

Browse structure collections

About this viewer

MolViewer shows 5UMN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.