Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 50.91 kDa 
• Atom Count: 3840 
• Residue Count: 445 
• Unique protein chains: 3

4HPO

Crystal structure of RV144-elicited antibody CH58 in complex with V2 peptide

• DOI: 10.2210/pdb4HPO/pdb

• Classification: Immune System/Viral Protein
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-10-24 Released: 2013-02-06 
• Deposition Author(s): McLellan, J.S., Gorman, J., Haynes, B.F., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.211 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2.

Liao, H.X., Bonsignori, M., Alam, S.M., McLellan, J.S., Tomaras, G.D., Moody, M.A., Kozink, D.M., Hwang, K.K., Chen, X., Tsao, C.Y., Liu, P., Lu, X., Parks, R.J., Montefiori, D.C., Ferrari, G., Pollara, J., Rao, M., Peachman, K.K., Santra, S., Letvin, N.L., Karasavvas, N., Yang, Z.Y., Dai, K., Pancera, M., Gorman, J., Wiehe, K., Nicely, N.I., Rerks-Ngarm, S., Nitayaphan, S., Kaewkungwal, J., Pitisuttithum, P., Tartaglia, J., Sinangil, F., Kim, J.H., Michael, N.L., Kepler, T.B., Kwong, P.D., Mascola, J.R., Nabel, G.J., Pinter, A., Zolla-Pazner, S., Haynes, B.F.

(2013) Immunity 38: 176-186

• PubMed: 23313589 
• DOI: 10.1016/j.immuni.2012.11.011
• Primary Citation of Related Structures:  
  4HPY, 4HPO, 4HQQ


• PubMed Abstract: 
  

The RV144 HIV-1 trial of the canary pox vector (ALVAC-HIV) plus the gp120 AIDSVAX B/E vaccine demonstrated an estimated efficacy of 31%, which correlated directly with antibodies to HIV-1 envelope variable regions 1 and 2 (V1-V2). Genetic analysis of trial viruses revealed increased vaccine efficacy against viruses matching the vaccine strain at V2 residue 169. Here, we isolated four V2 monoclonal antibodies from RV144 vaccinees that recognize residue 169, neutralize laboratory-adapted HIV-1, and mediate killing of field-isolate HIV-1-infected CD4(+) T cells. Crystal structures of two of the V2 antibodies demonstrated that residue 169 can exist within divergent helical and loop conformations, which contrasted dramatically with the β strand conformation previously observed with a broadly neutralizing antibody PG9. Thus, RV144 vaccine-induced immune pressure appears to target a region that may be both sequence variable and structurally polymorphic. Variation may signal sites of HIV-1 envelope vulnerability, providing vaccine designers with new options.

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Organizational Affiliation: 

Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CH58 Fab heavy chain	H	231	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CH58 Fab light chain	L	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	P	19	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for G9HS63 (Human immunodeficiency virus 1) Explore G9HS63  Go to UniProtKB:  G9HS63

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	A	2		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.211 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.594	α = 90
b = 75.804	β = 111.99
c = 54.688	γ = 90

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: 2012-10-24 
• Released Date: 2013-02-06 
Deposition Author(s): McLellan, J.S., Gorman, J., Haynes, B.F., Kwong, P.D.

Revision History 

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary