1HZH | pdb_00001hzh

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

• PDB DOI: https://doi.org/10.2210/pdb1HZH/pdb

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


• 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: 2.70 Å
• R-Value Free: 
  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1126/science.1061692
• Primary Citation Related Structures: 
  1HZH


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Macromolecule Content 

• Total Structure Weight: 151.63 kDa 
• Atom Count: 10,647 
• Modeled Residue Count: 1,331 
• Deposited Residue Count: 1,344 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN HEAVY CHAIN	A [auth H], B [auth K]	457	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN LIGHT CHAIN,Uncharacterized protein	C [auth L], D [auth M]	215	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A]	9		N/A
Glycosylation Resources
GlyTouCan: G36191CD GlyCosmos: G36191CD GlyGen: G36191CD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth B]	9		N/A
Glycosylation Resources
GlyTouCan: G27919IH GlyCosmos: G27919IH GlyGen: G27919IH

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 271.32	α = 90
b = 271.32	β = 90
c = 175.18	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2013-01-30
  Changes: Structure summary
• Version 1.4: 2017-06-28
  Changes: Advisory, Database references, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2026-03-04
  Changes: Refinement description