› 6mid

Electron Microscopy
4Å resolution

Cryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195

Released:
DOI: 10.2210/pdb6mid/pdb
PDB entry 6mid coloured by chain, front view.
PDB entry 6mid coloured by chain, side view.
PDB entry 6mid coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope.
Long F, Doyle M, Fernandez E, Miller AS, Klose T, Sevvana M, Bryan A, Davidson E, Doranz BJ, Kuhn RJ, Diamond MS, Crowe JE, Rossmann MG
Proc Natl Acad Sci U S A 116 1591-1596 (2019)
PMID: 30642974
Related structures: EMD-9131

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 480-mer (preferred)
PDBe Complex ID:
PDB-CPX-207175 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Envelope protein E Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 504 amino acids
Theoretical weight: 54.44 KDa
Source organism: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
UniProt:
  • Canonical: A0A024B7W1 (Residues: 291-794; Coverage: 15%)
Sequence domains:
Structure domains:
Small envelope protein M Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 75 amino acids
Theoretical weight: 8.5 KDa
Source organism: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
UniProt:
  • Canonical: A0A024B7W1 (Residues: 216-290; Coverage: 2%)
Sequence domains: Flavivirus envelope glycoprotein M
Structure domains: Flavivirus envelope glycoprotein M-like
monoclonal antibody ZIKV-195 heavy chain Chain: H
Molecule details ›
Chain: H
Length: 128 amino acids
Theoretical weight: 14.15 KDa
Source organism: Homo sapiens
Immunoglobulin lambda variable 1-36 Chain: L
Molecule details ›
Chain: L
Length: 110 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: A0A0B4J1U3 (Residues: 20-115; Coverage: 98%)
Gene name: IGLV1-36
Sequence domains: Immunoglobulin V-set domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4Å
Relevant EMDB volumes: EMD-9131

Quick links

Citations

8 review citations

Zika virus serological diagnosis: commercial tests and monoclonal antibodies as tools.
Silva et al. (2020)
7 more

5 mentions without citation

Phytocompounds of Rheum emodi, Thymus serpyllum, and Artemisia annua Inhibit Spike Protein of SARS-CoV-2 Binding to ACE2 Receptor: In Silico Approach.
Rolta et al. (2021)
4 more