3CLE | pdb_00003cle

HIV neutralizing monoclonal antibody YZ23

• PDB DOI: https://doi.org/10.2210/pdb3CLE/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2008-03-18 Released: 2008-03-25 
• Deposition Author(s): Jin, L., Paul, S., Symersky, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.272 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

HIV neutralizing monoclonal antibody YZ23

Nishiama, Y., Planque, S., Mitsuda, Y., Taguchi, H., Jin, L., Symersky, J., Boivin, S., Salas, M., Hanson, C., Paul, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.15 kDa 
• Atom Count: 3,354 
• Modeled Residue Count: 430 
• Deposited Residue Count: 434 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	A [auth L]	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain	B [auth H]	220	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.272 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.29	α = 90
b = 62.919	β = 90
c = 135.172	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Jin, L., Paul, S., Symersky, J.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary