2D1K

Ternary complex of the WH2 domain of mim with actin-dnase I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural basis for the actin-binding function of missing-in-metastasis

Lee, S.H.Kerff, F.Chereau, D.Ferron, F.Klug, A.Dominguez, R.

(2007) Structure 15: 145-155

  • DOI: 10.1016/j.str.2006.12.005
  • Primary Citation of Related Structures:  
    2D1K, 2D1L

  • PubMed Abstract: 
  • The adaptor protein missing-in-metastasis (MIM) contains independent F- and G-actin binding domains, consisting, respectively, of an N-terminal 250 aa IRSp53/MIM homology domain (IMD) and a C-terminal WASP-homology domain 2 (WH2). We determined the crystal structures of MIM's IMD and that of its WH2 bound to actin ...

    The adaptor protein missing-in-metastasis (MIM) contains independent F- and G-actin binding domains, consisting, respectively, of an N-terminal 250 aa IRSp53/MIM homology domain (IMD) and a C-terminal WASP-homology domain 2 (WH2). We determined the crystal structures of MIM's IMD and that of its WH2 bound to actin. The IMD forms a dimer, with each subunit folded as an antiparallel three-helix bundle. This fold is related to that of the BAR domain. Like the BAR domain, the IMD has been implicated in membrane binding. Yet, comparison of the structures reveals that the membrane binding surfaces of the two domains have opposite curvatures, which may determine the type of curvature of the interacting membrane. The WH2 of MIM is longer than the prototypical WH2, interacting with all four subdomains of actin. We characterize a similar WH2 at the C terminus of IRSp53 and propose that in these two proteins WH2 performs a scaffolding function.


    Organizational Affiliation

    Department of Physiology, University of Pennsylvania School of Medicine, 3700 Hamilton Walk, Philadelphia, PA 19104, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleA375Oryctolagus cuniculusMutation(s): 1 
Gene Names: ACTA1ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
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Go to UniProtKB:  P68135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyribonuclease-1B260Bos taurusMutation(s): 0 
Gene Names: DNASE1DNL1
EC: 3.1.21.1
UniProt
Find proteins for P00639 (Bos taurus)
Explore P00639 
Go to UniProtKB:  P00639
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UniProt GroupP00639
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Metastasis suppressor protein 1C32N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O43312 (Homo sapiens)
Explore O43312 
Go to UniProtKB:  O43312
PHAROS:  O43312
GTEx:  ENSG00000170873 
Entity Groups  
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UniProt GroupO43312
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
A L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.093α = 90
b = 75.487β = 90
c = 228.991γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary