4D07

DYNLL2 dynein light chain binds to an extended, unstructured linear motif of myosin 5a tail


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dynll2 Dynein Light Chain Binds to an Extended Linear Motif of Myosin 5A Tail that Has Structural Plasticity.

Bodor, A.Radnai, L.Hetenyi, C.Rapali, P.Lang, A.Kover, K.E.Perczel, A.Wahlgren, W.Y.Katona, G.Nyitray, L.

(2014) Biochemistry 53: 7107

  • DOI: 10.1021/bi500574z

  • PubMed Abstract: 
  • LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide ...

    LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide a profound characterization of the DYNLL2 binding motif of myo5a in free and DYNLL2-bound form by using nuclear magnetic resonance spectroscopy, X-ray crystallography, and molecular dynamics simulations. In the free form, the DYNLL2 binding region, located in an intrinsically disordered domain of the myo5a tail, has a nascent helical character. The motif becomes structured and folds into a β-strand upon binding to DYNLL2. Despite differences of the myo5a sequence from the consensus binding motif, one peptide is accommodated in each of the parallel DYNLL2 binding grooves, as for all other known partners. Interestingly, while the core motif shows a similar interaction pattern in the binding groove as seen in other complexes, the flanking residues make several additional contacts, thereby lengthening the binding motif. The N-terminal extension folds back and partially blocks the free edge of the β-sheet formed by the binding motif itself. The C-terminal extension contacts the dimer interface and interacts with symmetry-related residues of the second myo5a peptide. The involvement of flanking residues of the core binding site of myo5a could modify the quaternary structure of the full-length myo5a and affect its biological functions. Our results deepen the knowledge of the diverse partner recognition of DYNLL proteins and provide an example of a Janus-faced linear motif.


    Organizational Affiliation

    Laboratory of Structural Chemistry and Biology, Institute of Chemistry, and ‡Department of Biochemistry, Eötvös Loránd University , Budapest, 1117 Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
A
92Homo sapiensMutation(s): 0 
Gene Names: DYNLL2 (DLC2)
Find proteins for Q96FJ2 (Homo sapiens)
Go to Gene View: DYNLL2
Go to UniProtKB:  Q96FJ2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MYOSIN VA VARIANT
B
27Homo sapiensMutation(s): 0 
Gene Names: MYO5A (MYH12)
Find proteins for Q9Y4I1 (Homo sapiens)
Go to Gene View: MYO5A
Go to UniProtKB:  Q9Y4I1
Small Molecules
Ligands 3 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
CO
Query on CO

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Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 45.160α = 90.00
b = 45.160β = 90.00
c = 204.010γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Database references
  • Version 1.2: 2014-12-03
    Type: Database references