5VIG: Anti-Zika antibody Z006

Crystal structure of anti-Zika antibody Z006 bound to Zika virus 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, Zika virus
Chains: 6
Atoms: 7,905
Mol. weight: 121.1 kDa
Ligands: FLC
Released: 3 May 2017

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

Secondary structure: helices and β-sheets

5VIG contains 30 α-helices and 108 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 H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	57-59	3	17
α-helix	61-63	3
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-94	7	17
β-strand	102-103	2	17
β-strand	107-109	3	17
β-strand	110-111	2	16
β-strand	117	1	18
β-strand	120-124	5	19
β-strand	137-145	9	19
β-strand	146	1	18
β-strand	151-154	4	20
α-helix	155-157	3
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-183	8	19
α-helix	186-188	3
β-strand	195-200	6	20
α-helix	201-203	3
β-strand	205-210	6	20

Chains B and L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-14	5	8
β-strand	19-25	7	21
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	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	97-98	2	8
β-strand	102-107	6	8
β-strand	111	1	22
β-strand	115-118	4	23
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	23
β-strand	140	1	22
β-strand	144-150	7	24
β-strand	154	1	24
β-strand	159-163	5	23
α-helix	164-167	4
β-strand	173-182	10	23
α-helix	183-187	5
β-strand	192-198	7	24
β-strand	205-209	5	24

Chains G and Z: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	307	1	25
β-strand	312-320	9	26
β-strand	326-332	7	26
β-strand	339-340	2	25
β-strand	343-346	4	27
α-helix	353-354	2
β-strand	355	1	27
β-strand	357-358	2	26
β-strand	364-365	2	25
β-strand	372-379	8	26
β-strand	383-389	7	27
α-helix	392-394	3
β-strand	396-402	7	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	A, H	protein	232	Homo sapiens	S6B291 (AlphaFold model)
Fab light chain	B, L	protein	213	Homo sapiens	P0DOX7 (AlphaFold model)
Zika virus envelope protein DIII	G, Z	protein	110	Zika virus	A0A192GPS0

Sequence of entity 1 (A, H), FASTA

>5VIG_1 Fab heavy chain (chains A, H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFKNYAMAWVRQAPGKGLEWVSLLYNSEESTYY
ADSVKGRFTISRDNSKNTLFLQMNRLRVEDTAVYFCVRDRSNGWSSINLWGRGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 2 (B, L), FASTA

>5VIG_2 Fab light chain (chains B, L)
DIQMTQSPSTLSASVGDRVTMTCRASQTISGWLAWYQQKPGKAPKLLIYQASRLESGIPS
RFSGSGSGTEFTLTISSLQPDDVATYYCQQYSTFWTFGLGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (G, Z), FASTA

>5VIG_3 Zika virus envelope protein DIII (chains G, Z)
MRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGR
LITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTI

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	1

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

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