3REZ

glycoprotein GPIb variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Quaternary organization of GPIb-IX complex and insights into Bernard-Soulier syndrome revealed by the structures of GPIb beta and a GPIb beta/GPIX chimera

McEwan, P.A.Yang, W.Carr, K.H.Mo, X.Zheng, X.Li, R.Emsley, J.

(2011) Blood 118: 5292-5301

  • DOI: https://doi.org/10.1182/blood-2011-05-356253
  • Primary Citation of Related Structures:  
    3REZ, 3RFE

  • PubMed Abstract: 

    Platelet GPIb-IX receptor complex has 3 subunits GPIbα, GPIbβ, and GPIX, which assemble with a ratio of 1:2:1. Dysfunction in surface expression of the complex leads to Bernard-Soulier syndrome. We have crystallized the GPIbβ ectodomain (GPIbβ(E)) and determined the structure to show a single leucine-rich repeat with N- and C-terminal disulphide-bonded capping regions. The structure of a chimera of GPIbβ(E) and 3 loops (a,b,c) taken from the GPIX ectodomain sequence was also determined. The chimera (GPIbβ(Eabc)), but not GPIbβ(E), forms a tetramer in the crystal, showing a quaternary interface between GPIbβ and GPIX. Central to this interface is residue Tyr106 from GPIbβ, which inserts into a pocket generated by 2 loops (b,c) from GPIX. Mutagenesis studies confirmed this interface as a valid representation of interactions between GPIbβ and GPIX in the full-length complex. Eight GPIbβ missense mutations identified from patients with Bernard-Soulier syndrome were examined for changes to GPIb-IX complex surface expression. Two mutations, A108P and P74R, were found to maintain normal secretion/folding of GPIbβ(E) but were unable to support GPIX surface expression. The close structural proximity of these mutations to Tyr106 and the GPIbβ(E) interface with GPIX indicates they disrupt the quaternary organization of the GPIb-IX complex.


  • Organizational Affiliation

    Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet glycoprotein Ib beta chain, Platelet glycoprotein IX
A, B, C, D
129Homo sapiensMutation(s): 0 
Gene Names: GP1BBGP9
UniProt & NIH Common Fund Data Resources
Find proteins for P14770 (Homo sapiens)
Explore P14770 
Go to UniProtKB:  P14770
PHAROS:  P14770
GTEx:  ENSG00000169704 
Find proteins for P13224 (Homo sapiens)
Explore P13224 
Go to UniProtKB:  P13224
PHAROS:  P13224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP14770P13224
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
L [auth C],
O [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
K [auth C]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUL
Query on FUL

Download Ideal Coordinates CCD File 
I [auth C]beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
M [auth C]
N [auth C]
P [auth D]
F [auth A],
H [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D],
R [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.01α = 90
b = 72.01β = 90
c = 171.731γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary