1M10 | pdb_00001m10

Crystal structure of the complex of Glycoprotein Ib alpha and the von Willebrand Factor A1 Domain

• PDB DOI: https://doi.org/10.2210/pdb1M10/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris, Mesocricetus auratus
• Mutation(s): Yes 


• Deposited: 2002-06-16 Released: 2002-08-28 
• Deposition Author(s): Huizinga, E.G., Tsuji, S., Romijn, R.A.P., Schiphorst, M.E., de Groot, P.G., Sixma, J.J., Gros, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.296 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Models: experimental

Literature

Structures of glycoprotein Ibalpha and its complex with von Willebrand factor A1 domain.

Huizinga, E.G., Tsuji, S., Romijn, R.A., Schiphorst, M.E., de Groot, P.G., Sixma, J.J., Gros, P.

(2002) Science 297: 1176-1179

• PubMed: 12183630 
• DOI: https://doi.org/10.1126/science.107355
• Primary Citation Related Structures: 
  1M0Z, 1M10


• PubMed Abstract: 
  

  Transient interactions of platelet-receptor glycoprotein Ibalpha (GpIbalpha) and the plasma protein von Willebrand factor (VWF) reduce platelet velocity at sites of vascular damage and play a role in haemostasis and thrombosis. Here we present structures of the GpIbalpha amino-terminal domain and its complex with the VWF domain A1. In the complex, GpIbalpha wraps around one side of A1, providing two contact areas bridged by an area of solvated charge interaction. The structures explain the effects of gain-of-function mutations related to bleeding disorders and provide a model for shear-induced activation. These detailed insights into the initial interactions in platelet adhesion are relevant to the development of antithrombotic drugs.

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Organizational Affiliation: 
• Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.07 kDa 
• Atom Count: 3,688 
• Modeled Residue Count: 466 
• Deposited Residue Count: 498 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Willebrand Factor	A	208	Homo sapiens	Mutation(s): 1  Gene Names: VWF
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	Sequence Length	Organism	Details	Image
Glycoprotein Ib alpha	B	290	Homo sapiens	Mutation(s): 3  Gene Names: GP1BA
UniProt & NIH Common Fund Data Resources
Find proteins for P07359 (Homo sapiens) Explore P07359  Go to UniProtKB:  P07359
PHAROS:  P07359 GTEx:  ENSG00000185245

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.296 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.84	α = 90
b = 89.84	β = 90
c = 124.63	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-28 
Deposition Author(s): Huizinga, E.G., Tsuji, S., Romijn, R.A.P., Schiphorst, M.E., de Groot, P.G., Sixma, J.J., Gros, P.

Revision History  

• Version 1.0: 2002-08-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Data collection, Database references
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary