7K8Y Viral Protein Immune System date Sep 27, 2020
title Structure Of The Sars-Cov-2 S 2p Trimer In Complex With The Neutralizing Antibody Fab Fragment, C121 (State 2)
authors M.E.Abernathy, C.O.Barnes, P.J.Bjorkman
compound source
Molecule: Spike Glycoprotein
Chain: B, D, E
Synonym: S Glycoprotein,E2,Peplomer Protein
Engineered: Yes
Organism_scientific: Severe Acute Respiratory Syndrome Coro 2;
Organism_common: 2019-Ncov
Organism_taxid: 2697049
Gene: S, 2
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Hek293

Molecule: C121 Fab Heavy Chain
Chain: G
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Hek293

Molecule: C121 Fab Light Chain
Chain: I
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: Hek293
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.40 Å
ligand NAG enzyme
Primary referenceSARS-CoV-2 neutralizing antibody structures inform therapeutic strategies., Barnes CO, Jette CA, Abernathy ME, Dam KA, Esswein SR, Gristick HB, Malyutin AG, Sharaf NG, Huey-Tubman KE, Lee YE, Robbiani DF, Nussenzweig MC, West AP Jr, Bjorkman PJ, Nature. 2020 Oct 12. pii: 10.1038/s41586-020-2852-1. doi:, 10.1038/s41586-020-2852-1. PMID:33045718
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (490 Kb) [Save to disk]
  • Biological Unit Coordinates (7k8y.pdb1.gz) 470 Kb
  • LPC: Ligand-Protein Contacts for 7K8Y
  • CSU: Contacts of Structural Units for 7K8Y
  • Retrieve 7K8Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 7K8Y from S2C, [Save to disk]
  • View 7K8Y in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 7K8Y
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 7k8y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [7k8y_E] [7k8y_D] [7k8y_B] [7k8y_I] [7k8y_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 7K8Y
  • Community annotation for 7K8Y at PDBWiki (http://pdbwiki.org)

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