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: 94.92 kDa 
• Atom Count: 7150 
• Residue Count: 860 
• Unique protein chains: 2

6N35

Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

• DOI: 10.2210/pdb6N35/pdb
• Entry: 6N35 supersedes: 1OP3

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


• Deposited: 2018-11-14 Released: 2018-11-28 
• Deposition Author(s): Calarese, D.A., Stanfield, R.L., Wilson, I.A.
• 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: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Antibody domain exchange is an immunological solution to carbohydrate cluster recognition.

Calarese, D.A., Scanlan, C.N., Zwick, M.B., Deechongkit, S., Mimura, Y., Kunert, R., Zhu, P., Wormald, M.R., Stanfield, R.L., Roux, K.H., Kelly, J.W., Rudd, P.M., Dwek, R.A., Katinger, H., Burton, D.R., Wilson, I.A.

(2003) Science 300: 2065-2071

• PubMed: 12829775 
• DOI: 10.1126/science.1083182
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Human antibody 2G12 neutralizes a broad range of human immunodeficiency virus type 1 (HIV-1) isolates by binding an unusually dense cluster of carbohydrate moieties on the "silent" face of the gp120 envelope glycoprotein. Crystal structures of Fab 2G12 and its complexes with the disaccharide Manalpha1-2Man and with the oligosaccharide Man9GlcNAc2 revealed that two Fabs assemble into an interlocked VH domain-swapped dimer. Further biochemical, biophysical, and mutagenesis data strongly support a Fab-dimerized antibody as the prevalent form that recognizes gp120. The extraordinary configuration of this antibody provides an extended surface, with newly described binding sites, for multivalent interaction with a conserved cluster of oligomannose type sugars on the surface of gp120. The unique interdigitation of Fab domains within an antibody uncovers a previously unappreciated mechanism for high-affinity recognition of carbohydrate or other repeating epitopes on cell or microbial surfaces.

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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) Explore P0DOX7  Go to UniProtKB:  P0DOX7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab 2G12 heavy chain	H, M	224	Homo sapiens	Mutation(s): 0
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5

Oligosaccharides

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	A	2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	M	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BEZ	L	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
GOL	K	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.725	α = 90
b = 94.034	β = 90
c = 169.187	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-14 
• Released Date: 2018-11-28 
Deposition Author(s): Calarese, D.A., Stanfield, R.L., Wilson, I.A.
• This entry supersedes: 1OP3

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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: 2018-11-28
  Type: Initial release
  
• Version 1.1: 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