5VIC: Anti-Zika antibody Z004

Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII. Determined by X-ray diffraction at 3.0 Å resolution. Released 3 May 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Dengue virus type 1 (strain Nauru/West Pac/1974)
Chains: 3
Atoms: 3,904
Mol. weight: 59.33 kDa
Released: 3 May 2017

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

Secondary structure: helices and β-sheets

5VIC contains 17 α-helices and 55 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 E: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	301	1	12
β-strand	305-311	7	13
β-strand	320-327	8	13
β-strand	333-334	2	12
β-strand	337-339	3	14
β-strand	350-351	2	13
β-strand	357-358	2	12
β-strand	365-370	6	13
β-strand	376-380	5	14
α-helix	383-385	3
β-strand	387-391	5	14

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11-12	2	2
β-strand	18-24	7	1
α-helix	29-31	3
β-strand	32-39	8	3
β-strand	45-51	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-98	11	3
β-strand	102-103	2	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	114-116	3
β-strand	117	1	4
β-strand	120-124	5	5
β-strand	138-145	8	5
β-strand	146	1	4
β-strand	151-154	4	6
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
α-helix	171	1
β-strand	176-182	7	5
α-helix	187-189	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
α-helix	96	1
β-strand	98	1	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
β-strand	159-160	2	10
β-strand	163	1	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	H	protein	234	Homo sapiens	S6B291 (AlphaFold model)
Fab light chain	L	protein	214	Homo sapiens	P0DOX7 (AlphaFold model)
Dengue 1 Envelope DIII domain	E	protein	99	Dengue virus type 1 (strain Nauru/West Pac/1974)	P17763 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5VIC_1 Fab heavy chain (chains H)
EVQLLESGGGLVQPGGSLRLTCATSGFTFRDYAMSWVRQAPGKGLEWVSSYSGIDDSTYY
ADSVKGRFTISRDNSKSTLSLHMNSLRAEDSALYFCAKDRGPRGVGELFDSWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 2 (L), FASTA

>5VIC_2 Fab light chain (chains L)
DIQMTQSPSTLSASVGDRVTITCRASQSISKWLAWYQQKPGKAPKLLIYTTSTLKSGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCQHFYSVPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E), FASTA

>5VIC_3 Dengue 1 Envelope DIII domain (chains E)
SYVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPI
VTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKGS

Primary citation

Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico. Robbiani, D.F., Bozzacco, L., Keeffe, J.R. et al. Cell (2017) 169:597-609.e11. DOI 10.1016/j.cell.2017.04.024 · PubMed

Other PDB entries of the same protein (UniProt S6B291 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLY 1.6 Å, Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns…
3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6B9Z 1.82 Å, Trastuzumab Fab v3
4LLW 1.95 Å, Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A
6BAE 2.14 Å, Trastuzumab Fab v3 in complex with CQFDLSTRRLKC
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
5VEB 2.34 Å, Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6
6AZK 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine…
6AYN 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine…
6AZL 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope…
6AU5 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant
6AXP 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant

Browse structure collections

About this viewer

MolViewer shows 5VIC 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.