1GWB | pdb_00001gwb

STRUCTURE OF GLYCOPROTEIN 1B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.274 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Crystal Structure of the Platelet Glycoprotein Ib-Alpha N-Terminal Domain Reveals an Unmasking Mechanism of Receptor Activation

Uff, S.Clemetson, J.M.Harrison, T.Clemetson, K.J.Emsley, J.

(2002) J Biological Chem 277: 35657

  • DOI: https://doi.org/10.1074/jbc.M205271200
  • Primary Citation Related Structures: 
    1GWB

  • PubMed Abstract: 

    Glycoprotein Ib (GPIb) is a platelet receptor with a critical role in mediating the arrest of platelets at sites of vascular damage. GPIb binds to the A1 domain of von Willebrand factor (vWF-A1) at high blood shear, initiating platelet adhesion and contributing to the formation of a thrombus. To investigate the molecular basis of GPIb regulation and ligand binding, we have determined the structure of the N-terminal domain of the GPIb(alpha) chain (residues 1-279). This structure is the first determined from the cell adhesion/signaling class of leucine-rich repeat (LRR) proteins and reveals the topology of the characteristic disulfide-bonded flanking regions. The fold consists of an N-terminal beta-hairpin, eight leucine-rich repeats, a disulfide-bonded loop, and a C-terminal anionic region. The structure also demonstrates a novel LRR motif in the form of an M-shaped arrangement of three tandem beta-turns. Negatively charged binding surfaces on the LRR concave face and anionic region indicate two-step binding kinetics to vWF-A1, which can be regulated by an unmasking mechanism involving conformational change of a key loop. Using molecular docking of the GPIb and vWF-A1 crystal structures, we were also able to model the GPIb.vWF-A1 complex.


  • Organizational Affiliation
    • Department of Biochemistry, University of Leicester, Leicester LE1 7RH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 64.63 kDa 
  • Atom Count: 4,451 
  • Modeled Residue Count: 545 
  • Deposited Residue Count: 562 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PLATELET GLYCOPROTEIN IB ALPHA CHAIN
A, B
281Homo sapiensMutation(s): 0 
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: 2Go to GlyGen: P07359-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
J [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PT

Query on PT



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACY

Query on ACY



Download:Ideal Coordinates CCD File
E [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
A, B
L-PEPTIDE LINKINGC9 H11 N O6 STYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.274 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202α = 90
b = 202β = 90
c = 128γ = 120
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-06
    Type: Initial release
  • Version 1.1: 2011-10-19
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2012-01-18
    Changes: Other
  • Version 1.3: 2017-07-12
    Changes: Advisory
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-11-13
    Changes: Data collection, Database references, Structure summary