5FWW

Wnt modulator Kremen in complex with DKK1 (CRD2) and LRP6 (PE3PE4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.321 
  • R-Value Observed: 0.323 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight Into Ternary Complex Formation with Lrp6 and Dickkopf

Zebisch, M.Jackson, V.A.Zhao, Y.Jones, E.Y.

(2016) Structure 24: 1599

  • DOI: 10.1016/j.str.2016.06.020
  • Primary Citation of Related Structures:  
    5FWW, 5FWV, 5FWS, 5FWU, 5FWT

  • PubMed Abstract: 
  • Kremen 1 and 2 have been identified as co-receptors for Dickkopf (Dkk) proteins, hallmark secreted antagonists of canonical Wnt signaling. We present here three crystal structures of the ectodomain of human Kremen1 (KRM1ECD) at resolutions between 1.9 and 3 ...

    Kremen 1 and 2 have been identified as co-receptors for Dickkopf (Dkk) proteins, hallmark secreted antagonists of canonical Wnt signaling. We present here three crystal structures of the ectodomain of human Kremen1 (KRM1ECD) at resolutions between 1.9 and 3.2 Å. KRM1ECD emerges as a rigid molecule with tight interactions stabilizing a triangular arrangement of its Kringle, WSC, and CUB structural domains. The structures reveal an unpredicted homology of the WSC domain to hepatocyte growth factor. We further report the general architecture of the ternary complex formed by the Wnt co-receptor Lrp5/6, Dkk, and Krm, determined from a low-resolution complex crystal structure between β-propeller/EGF repeats (PE) 3 and 4 of the Wnt co-receptor LRP6 (LRP6PE3PE4), the cysteine-rich domain 2 (CRD2) of DKK1, and KRM1ECD. DKK1CRD2 is sandwiched between LRP6PE3 and KRM1Kringle-WSC. Modeling studies supported by surface plasmon resonance suggest a direct interaction site between Krm1CUB and Lrp6PE2.


    Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK. Electronic address: yvonne@strubi.ox.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6A619Homo sapiensMutation(s): 0 
Gene Names: LRP6
Find proteins for O75581 (Homo sapiens)
Explore O75581 
Go to UniProtKB:  O75581
NIH Common Fund Data Resources
PHAROS:  O75581
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
KREMEN PROTEIN 1B293Homo sapiensMutation(s): 0 
Gene Names: KREMEN1KREMENKRM1
Find proteins for Q96MU8 (Homo sapiens)
Explore Q96MU8 
Go to UniProtKB:  Q96MU8
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PHAROS:  Q96MU8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DICKKOPF-RELATED PROTEIN 1C85Homo sapiensMutation(s): 0 
Gene Names: DKK1UNQ492/PRO1008
Find proteins for O94907 (Homo sapiens)
Explore O94907 
Go to UniProtKB:  O94907
NIH Common Fund Data Resources
PHAROS:  O94907
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.355 
  • R-Value Work: 0.321 
  • R-Value Observed: 0.323 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.933α = 90
b = 100.08β = 90
c = 270.728γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references