Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 96.37 kDa 
• Atom Count: 6705 
• Residue Count: 869 
• Unique protein chains: 2

6MUB

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

• DOI: 10.2210/pdb6MUB/pdb
• Entry: 6MUB supersedes: 1ZLU

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


• Deposited: 2018-10-22 Released: 2018-10-31 
• Deposition Author(s): Wilson, I.A., Calarese, D.A., Stanfield, R.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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 

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

• PubMed: 16174734 
• DOI: 10.1073/pnas.0505763102
• Structures With Same Primary Citation


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab 2G12, light chain	K, L	213	Homo sapiens	Mutation(s): 0
Find proteins for P0DOX7 (Homo sapiens) Go to UniProtKB:  P0DOX7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab 2G12, heavy chain	H, M	226	Homo sapiens	Mutation(s): 0
Find proteins for P0DOX5 (Homo sapiens) Go to UniProtKB:  P0DOX5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	H, M	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	H, M	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

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 = 44.886	α = 90
b = 131.787	β = 90
c = 170.273	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-10-22 
• Released Date: 2018-10-31 
Deposition Author(s): Wilson, I.A., Calarese, D.A., Stanfield, R.L.
• This entry supersedes: 1ZLU

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM46192

Revision History 

• 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