Biological Assembly 1  

 3D View: Structure | Electron Density

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: 50.49 kDa 
• Atom Count: 3477 
• Modelled Residue Count: 464 
• Deposited Residue Count: 471 
• Unique protein chains: 2

4OCW

Crystal structure of human Fab CAP256-VRC26.06, a potent V1V2-directed HIV-1 neutralizing antibody

• DOI: 10.2210/pdb4OCW/pdb

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


• Deposited: 2014-01-09 Released: 2014-02-26 
• Deposition Author(s): Gorman, J., Doria-Rose, N.A., Schramm, C.A., Moore, P.L., Mascola, J.R., Shapiro, L., Morris, L., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies.

Doria-Rose, N.A., Schramm, C.A., Gorman, J., Moore, P.L., Bhiman, J.N., Dekosky, B.J., Ernandes, M.J., Georgiev, I.S., Kim, H.J., Pancera, M., Staupe, R.P., Altae-Tran, H.R., Bailer, R.T., Crooks, E.T., Cupo, A., Druz, A., Garrett, N.J., Hoi, K.H., Kong, R., Louder, M.K., Longo, N.S., McKee, K., Nonyane, M., O'Dell, S., Roark, R.S., Rudicell, R.S., Schmidt, S.D., Sheward, D.J., Soto, C., Wibmer, C.K., Yang, Y., Zhang, Z., Sequencing, Nisc Comparative, Mullikin, J.C., Binley, J.M., Sanders, R.W., Wilson, I.A., Moore, J.P., Ward, A.B., Georgiou, G., Williamson, C., Abdool Karim, S.S., Morris, L., Kwong, P.D., Shapiro, L., Mascola, J.R.

(2014) Nature 509: 55-62

• PubMed: 24590074 
• DOI: 10.1038/nature13036
• Primary Citation of Related Structures:  
  4OCR, 4OCS, 4OCW, 4OD1, 4OD3, 4ODH, 4ORG


• PubMed Abstract: 
  

Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development.

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Organizational Affiliation: 

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAP256-VRC26.06 light chain	A [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAP256-VRC26.06 heavy chain	B [auth H]	257	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	B [auth H]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 253.514	α = 90
b = 253.514	β = 90
c = 70.05	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-09 
• Released Date: 2014-02-26 
Deposition Author(s): Gorman, J., Doria-Rose, N.A., Schramm, C.A., Moore, P.L., Mascola, J.R., Shapiro, L., Morris, L., Kwong, P.D.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2014-04-02
  Changes: Database references
• Version 1.2: 2014-05-14
  Changes: Database references