Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 151917.23 
• Atom Count: 10576 
• Residue Count: 1344 
• Unique protein chains: 2

1HZH

CRYSTAL STRUCTURE OF THE INTACT HUMAN IGG B12 WITH BROAD AND POTENT ACTIVITY AGAINST PRIMARY HIV-1 ISOLATES: A TEMPLATE FOR HIV VACCINE DESIGN

• DOI: 10.2210/pdb1HZH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus


• Deposited: 2001-01-24 Released: 2001-08-15 
• Deposition Author(s): Saphire, E.O., Burton, D.R., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.273 
• R-Value Work: 0.229 

Literature

Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design.

Saphire, E.O., Parren, P.W., Pantophlet, R., Zwick, M.B., Morris, G.M., Rudd, P.M., Dwek, R.A., Stanfield, R.L., Burton, D.R., Wilson, I.A.

(2001) Science 293: 1155-1159

• PubMed: 11498595 
• DOI: 10.1126/science.1061692


• PubMed Abstract: 
  

We present the crystal structure at 2.7 angstrom resolution of the human antibody IgG1 b12. Antibody b12 recognizes the CD4-binding site of human immunodeficiency virus-1 (HIV-1) gp120 and is one of only two known antibodies against gp120 capable of broad and potent neutralization of primary HIV-1 isolates. A key feature of the antibody-combining site is the protruding, finger-like long CDR H3 that can penetrate the recessed CD4-binding site of gp120. A docking model of b12 and gp120 reveals severe structural constraints that explain the extraordinary challenge in eliciting effective neutralizing antibodies similar to b12. The structure, together with mutagenesis studies, provides a rationale for the extensive cross-reactivity of b12 and a valuable framework for the design of HIV-1 vaccines capable of eliciting b12-like activity.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
IMMUNOGLOBULIN HEAVY CHAIN	H, K	457	Homo sapiens	Mutation(s): 0  Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens) Go to UniProtKB:  P01857

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein	L, M	215	Homo sapiens	Mutation(s): 0  Gene Names: IGKC
Find proteins for P01834 (Homo sapiens) Go to UniProtKB:  P01834

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MAN	H, K	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	K	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
GAL	H, K	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
BMA	H, K	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NAG	H, K	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.273 
• R-Value Work: 0.229 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 271.320	α = 90.00
b = 271.320	β = 90.00
c = 175.180	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-01-24 
• Released Date: 2001-08-15 
• Deposition Author(s): Saphire, E.O., Burton, D.R., Wilson, I.A.

Revision History 

• Version 1.0: 2001-08-15
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2013-01-30
  Type: Structure summary
• Version 1.4: 2017-06-28
  Type: Advisory, Database references, Source and taxonomy, Structure summary