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: 1.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    2FD6

  • 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 at 1 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase-type plasminogen activatorA122Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  P00749
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
L chain of Fab of ATN-615 anti-uPAR antibodyB [auth L]214Mus musculusMutation(s): 0 
Gene Names: Igkv8-30Gm10883
Find proteins for Q52L64 (Mus musculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
H chain of Fab of ATN-615 anti-uPAR antibodyC [auth H]213Mus musculusMutation(s): 0 
Gene Names: V165-D-J-C mu
Find proteins for Q924Q0 (Mus musculus)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase plasminogen activator surface receptorD [auth U]276Homo sapiensMutation(s): 0 
Gene Names: PLAURMO3UPAR
Find proteins for Q03405 (Homo sapiens)
Explore Q03405 
Go to UniProtKB:  Q03405
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PHAROS:  Q03405
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth B]2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth C]2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

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N [auth U]2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
PG4
Query on PG4

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O [auth U]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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M [auth H]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ETX
Query on ETX

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H [auth L], J [auth L], K [auth H]2-ETHOXYETHANOL
C4 H10 O2
ZNQVEEAIQZEUHB-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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I [auth L], L [auth H]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.792α = 90
b = 86.805β = 94.54
c = 124.69γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2012-07-18
    Changes: Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary