6MTS | pdb_00006mts

Crystal structure of VRC43.03 Fab

• PDB DOI: https://doi.org/10.2210/pdb6MTS/pdb

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


• Deposited: 2018-10-21 Released: 2019-03-27 
• Deposition Author(s): Kwon, Y.D., Druz, A., Law, W.H., Peng, D., Doria-Rose, N.A., Kwong, P.D.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual.

Krebs, S.J., Kwon, Y.D., Schramm, C.A., Law, W.H., Donofrio, G., Zhou, K.H., Gift, S., Dussupt, V., Georgiev, I.S., Schatzle, S., McDaniel, J.R., Lai, Y.T., Sastry, M., Zhang, B., Jarosinski, M.C., Ransier, A., Chenine, A.L., Asokan, M., Bailer, R.T., Bose, M., Cagigi, A., Cale, E.M., Chuang, G.Y., Darko, S., Driscoll, J.I., Druz, A., Gorman, J., Laboune, F., Louder, M.K., McKee, K., Mendez, L., Moody, M.A., O'Sullivan, A.M., Owen, C., Peng, D., Rawi, R., Sanders-Buell, E., Shen, C.H., Shiakolas, A.R., Stephens, T., Tsybovsky, Y., Tucker, C., Verardi, R., Wang, K., Zhou, J., Zhou, T., Georgiou, G., Alam, S.M., Haynes, B.F., Rolland, M., Matyas, G.R., Polonis, V.R., McDermott, A.B., Douek, D.C., Shapiro, L., Tovanabutra, S., Michael, N.L., Mascola, J.R., Robb, M.L., Kwong, P.D., Doria-Rose, N.A.

(2019) Immunity 50: 677-691.e13

• PubMed: 30876875 
• DOI: https://doi.org/10.1016/j.immuni.2019.02.008
• Primary Citation Related Structures: 
  6MTO, 6MTP, 6MTQ, 6MTR, 6MTS, 6MTT


• PubMed Abstract: 
  

  Lineage-based vaccine design is an attractive approach for eliciting broadly neutralizing antibodies (bNAbs) against HIV-1. However, most bNAb lineages studied to date have features indicative of unusual recombination and/or development. From an individual in the prospective RV217 cohort, we identified three lineages of bNAbs targeting the membrane-proximal external region (MPER) of the HIV-1 envelope. Antibodies RV217-VRC42.01, -VRC43.01, and -VRC46.01 used distinct modes of recognition and neutralized 96%, 62%, and 30%, respectively, of a 208-strain virus panel. All three lineages had modest levels of somatic hypermutation and normal antibody-loop lengths and were initiated by the founder virus MPER. The broadest lineage, VRC42, was similar to the known bNAb 4E10. A multimeric immunogen based on the founder MPER activated B cells bearing the unmutated common ancestor of VRC42, with modest maturation of early VRC42 intermediates imparting neutralization breadth. These features suggest that VRC42 may be a promising template for lineage-based vaccine design.

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Organizational Affiliation: 
• U.S. Military HIV Research Program, WRAIR, Silver Spring, MD, USA; Henry Jackson Foundation, Bethesda, MD, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
Duke University School of Medicine and Center for HIV/AIDS Vaccine Immunology - Immunogen Discovery, Durham, NC, USA.
Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.
U.S. Military HIV Research Program, WRAIR, Silver Spring, MD, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Columbia University, New York, NY, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Columbia University, New York, NY, USA. Electronic address: [e-mail].
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 47.48 kDa 
• Atom Count: 3,322 
• Modeled Residue Count: 436 
• Deposited Residue Count: 444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody VRC43.03 Fab heavy chain	A [auth H]	229	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody VRC43.03 Fab light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.424	α = 90
b = 69.628	β = 90
c = 122.192	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Kwon, Y.D., Druz, A., Law, W.H., Peng, D., Doria-Rose, N.A., Kwong, P.D.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary