Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 89.80 kDa 
• Atom Count: 6237 
• Residue Count: 778 
• Unique protein chains: 3

4JB9

Crystal structure of antibody VRC06 in complex with HIV-1 gp120 core

• DOI: 10.2210/pdb4JB9/pdb

• Classification: viral protein/immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-02-19 Released: 2013-05-08 
• Deposition Author(s): Kwon, Y.D., Zhou, T., Srivatsan, S., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

Literature

Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.

Georgiev, I.S., Doria-Rose, N.A., Zhou, T., Kwon, Y.D., Staupe, R.P., Moquin, S., Chuang, G.Y., Louder, M.K., Schmidt, S.D., Altae-Tran, H.R., Bailer, R.T., McKee, K., Nason, M., O'Dell, S., Ofek, G., Pancera, M., Srivatsan, S., Shapiro, L., Connors, M., Migueles, S.A., Morris, L., Nishimura, Y., Martin, M.A., Mascola, J.R., Kwong, P.D.

(2013) Science 340: 751-756

• PubMed: 23661761 
• DOI: 10.1126/science.1233989
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Serum characterization and antibody isolation are transforming our understanding of the humoral immune response to viral infection. Here, we show that epitope specificities of HIV-1-neutralizing antibodies in serum can be elucidated from the serum pattern of neutralization against a diverse panel of HIV-1 isolates. We determined "neutralization fingerprints" for 30 neutralizing antibodies on a panel of 34 diverse HIV-1 strains and showed that similarity in neutralization fingerprint correlated with similarity in epitope. We used these fingerprints to delineate specificities of polyclonal sera from 24 HIV-1-infected donors and a chimeric siman-human immunodeficiency virus-infected macaque. Delineated specificities matched published specificities and were further confirmed by antibody isolation for two sera. Patterns of virus-isolate neutralization can thus afford a detailed epitope-specific understanding of neutralizing-antibody responses to viral infection.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
clade A/E 93TH057 HIV-1 gp120 core	G	353	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for Q0ED31 (Human immunodeficiency virus 1) Explore Q0ED31  Go to UniProtKB:  Q0ED31

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
antibody VRC06 heavy chain	H	232	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
antibody VRC06 light chain	L	209	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.244	α = 90
b = 68.924	β = 90
c = 224.225	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-19 
• Released Date: 2013-05-08 
Deposition Author(s): Kwon, Y.D., Zhou, T., Srivatsan, S., Kwong, P.D.

Revision History 

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references
• Version 1.2: 2016-10-19
  Changes: Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary