1SVZ | pdb_00001svz

Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope peptide corresponding to N-terminus of HIV-2 protease

• PDB DOI: https://doi.org/10.2210/pdb1SVZ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-30 Released: 2005-03-01 
• Deposition Author(s): Rezacova, P., Brynda, J., Lescar, J., Bentley, G.A., Fabry, M., Horejsi, M., Sedlacek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a cross-reaction complex between an anti-HIV-1 protease antibody and an HIV-2 protease peptide

Rezacova, P., Brynda, J., Lescar, J., Fabry, M., Horejsi, M., Sieglova, I., Sedlacek, J., Bentley, G.A.

(2005) J Struct Biol 149: 332-337

• PubMed: 15721587 
• DOI: https://doi.org/10.1016/j.jsb.2004.11.009
• Primary Citation Related Structures: 
  1SVZ


• PubMed Abstract: 
  

  The monoclonal antibody 1696, elicited by HIV-1 protease, inhibits the activity of both HIV-1 and HIV-2 proteases with inhibition constants in the low nanomolar range. The antibody cross-reacts with peptides derived from the N-terminal region of both proteases. The crystal structure of the recombinant single-chain Fv fragment of 1696 complexed with an N-terminal peptide from the HIV-2 protease has been determined at 1.88A resolution. Interactions of the peptide with scFv1696 are compared with the previously reported structure of scFv1696 in complex with the corresponding peptide from HIV-1 protease. The origin of cross-reactivity of mAb1696 with HIV proteases is discussed.

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Organizational Affiliation: 
• Department of Recombinant Expression and Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 37 Prague 6, Czech Republic. [e-mail]

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.

Macromolecule Content 

• Total Structure Weight: 55.88 kDa 
• Atom Count: 4,146 
• Modeled Residue Count: 476 
• Deposited Residue Count: 510 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
single-chain Fv fragment 1696	A, B	247	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01631 (Mus musculus) Explore P01631  Go to UniProtKB:  P01631

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
epitope peptide corresponding to N-terminus of HIV-2 protease	C, D	8	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.184	α = 90
b = 56.413	β = 102.13
c = 88.304	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Rezacova, P., Brynda, J., Lescar, J., Bentley, G.A., Fabry, M., Horejsi, M., Sedlacek, J.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary