4NHG

Crystal Structure of 2G12 IgG Dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.00 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.359 
  • R-Value Observed: 0.360 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for enhanced HIV-1 neutralization by a dimeric immunoglobulin G form of the glycan-recognizing antibody 2G12.

Wu, Y.West, A.P.Kim, H.J.Thornton, M.E.Ward, A.B.Bjorkman, P.J.

(2013) Cell Rep 5: 1443-1455

  • DOI: 10.1016/j.celrep.2013.11.015
  • Primary Citation of Related Structures:  
    4NHG, 4NHH

  • PubMed Abstract: 
  • The human immunoglobulin G (IgG) 2G12 recognizes high-mannose carbohydrates on the HIV type 1 (HIV-1) envelope glycoprotein gp120. Its two antigen-binding fragments (Fabs) are intramolecularly domain exchanged, resulting in a rigid (Fab)2 unit including a third antigen-binding interface not found in antibodies with flexible Fab arms ...

    The human immunoglobulin G (IgG) 2G12 recognizes high-mannose carbohydrates on the HIV type 1 (HIV-1) envelope glycoprotein gp120. Its two antigen-binding fragments (Fabs) are intramolecularly domain exchanged, resulting in a rigid (Fab)2 unit including a third antigen-binding interface not found in antibodies with flexible Fab arms. We determined crystal structures of dimeric 2G12 IgG created by intermolecular domain exchange, which exhibits increased breadth and >50-fold increased neutralization potency compared with monomeric 2G12. The four Fab and two fragment crystalline (Fc) regions of dimeric 2G12 were localized at low resolution in two independent structures, revealing IgG dimers with two (Fab)2 arms analogous to the Fabs of conventional monomeric IgGs. Structures revealed three conformationally distinct dimers, demonstrating flexibility of the (Fab)2-Fc connections that was confirmed by electron microscopy, small-angle X-ray scattering, and binding studies. We conclude that intermolecular domain exchange, flexibility, and bivalent binding to allow avidity effects are responsible for the increased potency and breadth of dimeric 2G12.


    Organizational Affiliation

    Division of Biology and Biological Engineering 114-96, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. Electronic address: bjorkman@caltech.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2G12 IgG dimer heavy chainA, D, E, M [auth H], H [auth I], P [auth M]243Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
2G12 IgG dimer light chainB, C, F, G, N [auth K], O [auth L]213Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatitis B virus receptor binding proteinI [auth J], J [auth N], Q [auth O], R [auth P], K [auth X], L [auth Y]211Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q6PYX1 (Homo sapiens)
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Go to UniProtKB:  Q6PYX1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.00 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.359 
  • R-Value Observed: 0.360 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 246.25α = 90
b = 246.25β = 90
c = 657.31γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Structure summary
  • Version 1.2: 2019-07-17
    Changes: Advisory, Data collection, Refinement description