7F49

von Willebrand factor (VWF) A1 domain with BT-100 aptamer RNA

• PDB DOI: https://doi.org/10.2210/pdb7F49/pdb
• NAKB: 7F49

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-06-18 Released: 2021-07-07 
• Deposition Author(s): Zhu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

The development and characterization of a long acting anti-thrombotic von Willebrand factor (VWF) aptamer

Zhu, S., Gilbert, C.J.

(2020) J Thromb Haemost 18: 1113-1123

• PubMed: 32011054 
• DOI: https://doi.org/10.1111/jth.14755
• Primary Citation of Related Structures:  
  7F49


• PubMed Abstract: 
  

  Thrombus formation involves coagulation proteins and platelets. The latter, referred to as platelet-mediated thrombogenesis, is predominant in arterial circulation. Platelet thrombogenesis follows vascular injury when extracellular von Willebrand factor (VWF) binds via its A3 domain to exposed collagen, and the free VWF A1 domain binds to platelet glycoprotein Ib (GPIb).

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Organizational Affiliation: 

Guardian Therapeutics Inc, Lexington, Massachusetts, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.12 kDa 
• Atom Count: 2,400 
• Modelled Residue Count: 228 
• Deposited Residue Count: 240 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Willebrand factor	A	210	Homo sapiens	Mutation(s): 1  Gene Names: VWF, F8VWF
UniProt & NIH Common Fund Data Resources
Find proteins for P04275 (Homo sapiens) Explore P04275  Go to UniProtKB:  P04275
PHAROS:  P04275 GTEx:  ENSG00000110799

Entity ID: 2
Molecule	Chains	Length	Organism	Image
BT-100	B	30	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.98	α = 90
b = 122.404	β = 90
c = 42.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Zhu, S.

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description