6MUB

Anti-HIV-1 Fab 2G12 + Man5 re-refinement

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12.

Calarese, D.A., Lee, H.K., Huang, C.Y., Best, M.D., Astronomo, R.D., Stanfield, R.L., Katinger, H., Burton, D.R., Wong, C.H., Wilson, I.A.

(2005) Proc Natl Acad Sci U S A 102: 13372-13377

  • DOI: 10.1073/pnas.0505763102
  • Primary Citation of Related Structures:  
    6MNF, 6MSY, 6MU3, 6MUB

  • PubMed Abstract: 

    • Human antibody 2G12 neutralizes a broad range of HIV-1 isolates. Hence, molecular characterization of its epitope, which corresponds to a conserved cluster of oligomannoses on the viral envelope glycoprotein gp120, is a high priority in HIV vaccine design ...

    Human antibody 2G12 neutralizes a broad range of HIV-1 isolates. Hence, molecular characterization of its epitope, which corresponds to a conserved cluster of oligomannoses on the viral envelope glycoprotein gp120, is a high priority in HIV vaccine design. A prior crystal structure of 2G12 in complex with Man(9)GlcNAc(2) highlighted the central importance of the D1 arm in antibody binding. To characterize the specificity of 2G12 more precisely, we performed solution-phase ELISA, carbohydrate microarray analysis, and cocrystallized Fab 2G12 with four different oligomannose derivatives (Man(4), Man(5), Man(7), and Man(8)) that compete with gp120 for binding to 2G12. Our combined studies reveal that 2G12 is capable of binding both the D1 and D3 arms of the Man(9)GlcNAc(2) moiety, which would provide more flexibility to make the required multivalent interactions between the antibody and the gp120 oligomannose cluster than thought previously. These results have important consequences for the design of immunogens to elicit 2G12-like neutralizing antibodies as a component of an HIV vaccine.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 2G12, light chainC [auth K],
A [auth L]		213Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX7 (Homo sapiens)
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Go to UniProtKB:  P0DOX7
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UniProt GroupP0DOX7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 2G12, heavy chainB [auth H],
D [auth M]		226Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
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UniProt GroupP0DOX5
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranoseE [auth A],
F [auth B]		5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G96586KV
GlyCosmos:  G96586KV
GlyGen:  G96586KV
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.886α = 90
b = 131.787β = 90
c = 170.273γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM46192

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary