5WHZ | pdb_00005whz

PGDM1400-10E8v4 CODV Fab

• PDB DOI: https://doi.org/10.2210/pdb5WHZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-07-18 Released: 2017-10-11 
• Deposition Author(s): Lord, D.M., Wei, R.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 
  0.287 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Models: experimental

Literature

Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques.

Xu, L., Pegu, A., Rao, E., Doria-Rose, N., Beninga, J., McKee, K., Lord, D.M., Wei, R.R., Deng, G., Louder, M., Schmidt, S.D., Mankoff, Z., Wu, L., Asokan, M., Beil, C., Lange, C., Leuschner, W.D., Kruip, J., Sendak, R., Do Kwon, Y., Zhou, T., Chen, X., Bailer, R.T., Wang, K., Choe, M., Tartaglia, L.J., Barouch, D.H., O'Dell, S., Todd, J.P., Burton, D.R., Roederer, M., Connors, M., Koup, R.A., Kwong, P.D., Yang, Z.Y., Mascola, J.R., Nabel, G.J.

(2017) Science 358: 85-90

• PubMed: 28931639 
• DOI: https://doi.org/10.1126/science.aan8630
• Primary Citation Related Structures: 
  5WHZ


• PubMed Abstract: 
  

  The development of an effective AIDS vaccine has been challenging because of viral genetic diversity and the difficulty of generating broadly neutralizing antibodies (bnAbs). We engineered trispecific antibodies (Abs) that allow a single molecule to interact with three independent HIV-1 envelope determinants: the CD4 binding site, the membrane-proximal external region (MPER), and the V1V2 glycan site. Trispecific Abs exhibited higher potency and breadth than any previously described single bnAb, showed pharmacokinetics similar to those of human bnAbs, and conferred complete immunity against a mixture of simian-human immunodeficiency viruses (SHIVs) in nonhuman primates, in contrast to single bnAbs. Trispecific Abs thus constitute a platform to engage multiple therapeutic targets through a single protein, and they may be applicable for treatment of diverse diseases, including infections, cancer, and autoimmunity.

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Organizational Affiliation: 
• Sanofi, 640 Memorial Drive, Cambridge, MA 02139, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
Department of Immunology and Microbiology, International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.
National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA. [e-mail] [e-mail].
Sanofi, 640 Memorial Drive, Cambridge, MA 02139, USA. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 80.4 kDa 
• Atom Count: 5,169 
• Modeled Residue Count: 677 
• Deposited Residue Count: 734 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-HIV CODV-Fab Light chain	A [auth L]	338	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-HIV CODV-Fab Heavy chain	B [auth H]	396	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free:  0.287 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.226	α = 90
b = 151.226	β = 90
c = 200.595	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Lord, D.M., Wei, R.R.

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary