Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 101.45 kDa 
• Atom Count: 6801 
• Residue Count: 829 
• Unique protein chains: 3

1JVQ

Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive loop peptide, and an exogenous tetrapeptide

• DOI: 10.2210/pdb1JVQ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2001-08-31 Released: 2003-06-03 
• Deposition Author(s): Zhou, A., Huntington, J.A., Lomas, D.A., Carrell, R.W., Stein, P.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.258 
• R-Value Work: 0.204 

Literature

How small peptides block and reverse serpin polymerisation

Zhou, A., Stein, P.E., Huntington, J.A., Sivasothy, P., Lomas, D.A., Carrell, R.W.

(2004) J Mol Biol 342: 931-941

• PubMed: 15342247 
• DOI: 10.1016/j.jmb.2004.07.078
• Primary Citation of Related Structures:  
  1JVQ


• PubMed Abstract: 
  

Many of the late-onset dementias, including Alzheimer's disease and the prion encephalopathies, arise from the aberrant aggregation of individual proteins. The serpin family of serine protease inhibitors provides a well-defined structural example of such pathological aggregation, as its mutant variants readily form long-chain polymers, resulting in diseases ranging from thrombosis to dementia. The intermolecular linkages result from the insertion of the reactive site loop of one serpin molecule into the middle strand (s4A) position of the A beta-sheet of another molecule. We define here the structural requirements for small peptides to competitively bind to and block the s4A position to prevent this intermolecular linkage and polymerisation. The entry and anchoring of blocking-peptides is facilitated by the presence of a threonine which inserts into the site equivalent to P8 of s4A. But the critical requirement for small blocking-peptides is demonstrated in crystallographic structures of the complexes formed with selected tri- and tetrapeptides. These structures indicate that the binding is primarily due to the insertion of peptide hydrophobic side-chains into the P4 and P6 sites of s4A. The findings allow the rational design of synthetic blocking-peptides small enough to be suitable for mimetic design. This is demonstrated here with a tetrapeptide that preferentially blocks the polymerisation of a pathologically unstable serpin commonly present in people of European descent.

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Organizational Affiliation: 

Departments of Haematology and Medicine, University of Cambridge, Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 2XY, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTITHROMBIN-III	I, L	432	Homo sapiens	Mutation(s): 0  Gene Names: SERPINC1, AT3, PRO0309
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
NIH Common Fund Data Resources
PHAROS  P01008 GTEx  ENSG00000117601

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P14-P8 reactive loop peptide	C	8	N/A	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
exogenous Cholecystokinin tetrapeptide	D	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	I, L	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	I	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.258 
• R-Value Work: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.144	α = 90
b = 100.622	β = 104.42
c = 87.157	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-31 
• Released Date: 2003-06-03 
Deposition Author(s): Zhou, A., Huntington, J.A., Lomas, D.A., Carrell, R.W., Stein, P.E.

Revision History 

• Version 1.0: 2003-06-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary