2FD6

Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structure of human urokinase plasminogen activator in complex with its receptor

Huai, Q., Mazar, A.P., Kuo, A., Parry, G.C., Shaw, D.E., Callahan, J., Li, Y., Yuan, C., Bian, C., Chen, L., Furie, B., Furie, B.C., Cines, D.B., Huang, M.

(2006) Science 311: 656-659

  • DOI: 10.1126/science.1121143

  • PubMed Abstract: 

    • The urokinase plasminogen activator binds to its cellular receptor with high affinity and initiates signaling cascades that are implicated in pathological processes including tumor growth, metastasis, and inflammation. We report the crystal structure ...

    The urokinase plasminogen activator binds to its cellular receptor with high affinity and initiates signaling cascades that are implicated in pathological processes including tumor growth, metastasis, and inflammation. We report the crystal structure at 1.9 angstroms of the urokinase receptor complexed with the urokinase amino-terminal fragment and an antibody against the receptor. The three domains of urokinase receptor form a concave shape with a central cone-shaped cavity where the urokinase fragment inserts. The structure provides insight into the flexibility of the urokinase receptor that enables its interaction with a wide variety of ligands and a basis for the design of urokinase-urokinase receptor antagonists.

    Organizational Affiliation: 

    Division of Hemostasis and Thrombosis, Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urokinase-type plasminogen activator
A
122Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Go to Gene View: PLAU
Go to UniProtKB:  P00749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
L chain of Fab of ATN-615 anti-uPAR antibody
L
214Mus musculusMutation(s): 0 
Gene Names: Igkv8-30 (Gm10883)
Find proteins for Q52L64 (Mus musculus)
Go to UniProtKB:  Q52L64
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
H chain of Fab of ATN-615 anti-uPAR antibody
H
213Mus musculusMutation(s): 0 
Gene Names: V165-D-J-C mu
Find proteins for Q924Q0 (Mus musculus)
Go to UniProtKB:  Q924Q0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Urokinase plasminogen activator surface receptor
U
276Homo sapiensMutation(s): 0 
Gene Names: PLAUR (MO3, UPAR)
Find proteins for Q03405 (Homo sapiens)
Go to Gene View: PLAUR
Go to UniProtKB:  Q03405
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FUC
Query on FUC
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Download CCD File 
U
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
EDO
Query on EDO
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Download CCD File 
H, L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4
Download SDF File 
Download CCD File 
U
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE
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Download CCD File 
H
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG
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Download CCD File 
U
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
U
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ETX
Query on ETX
Download SDF File 
Download CCD File 
H, L
2-ETHOXYETHANOL
C4 H10 O2
ZNQVEEAIQZEUHB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.792α = 90.00
b = 86.805β = 94.54
c = 124.690γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2012-07-18
    Type: Derived calculations