1P9A | pdb_00001p9a

Crystal Structure of N-Terminal Domain of Human Platelet Receptor Glycoprotein Ib-alpha at 1.7 Angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.224 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1P9A

This is version 2.3 of the entry. See complete history

Literature

Modulation of alpha-thrombin function by distinct interactions with platelet glycoprotein Ibalpha

Celikel, R.McClintock, R.A.Roberts, J.R.Mendolicchio, G.L.Ware, J.Varughese, K.I.Ruggeri, Z.M.

(2003) Science 301: 218-221

  • DOI: https://doi.org/10.1126/science.1084183
  • Primary Citation Related Structures: 
    1OOK, 1P9A

  • PubMed Abstract: 

    Thrombin bound to platelets contributes to stop bleeding and, in pathological conditions, may cause vascular thrombosis. We have determined the structure of platelet glycoprotein Ibalpha (GpIbalpha) bound to thrombin at 2.3 angstrom resolution and defined two sites in GpIbalpha that bind to exosite II and exosite I of two distinct alpha-thrombin molecules, respectively. GpIbalpha occupancy may be sequential, as the site binding to alpha-thrombin exosite I appears to be cryptic in the unoccupied receptor but exposed when a first thrombin molecule is bound through exosite II. These interactions may modulate alpha-thrombin function by mediating GpIbalpha clustering and cleavage of protease-activated receptors, which promote platelet activation, while limiting fibrinogen clotting through blockade of exosite I.


  • Organizational Affiliation
    • Roon Research Center for Arteriosclerosis and Thrombosis, Division of Experimental Thrombosis and Hemostasis, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 33.06 kDa 
  • Atom Count: 2,334 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 290 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Platelet glycoprotein Ib alpha chain precursorA [auth G]290Homo sapiensMutation(s): 1 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07359
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P07359-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G31886NL
GlyCosmos: G31886NL
GlyGen: G31886NL

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.224 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.734α = 90
b = 51.734β = 90
c = 114.041γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-27
    Changes: Database references, Structure summary
  • Version 2.2: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-13
    Changes: Structure summary