4KP3 | pdb_00004kp3

Crystal Structure of MyoVa-GTD in Complex with Two Cargos


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.241 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural basis of cargo recognitions for class V myosins

Wei, Z.Liu, X.Yu, C.Zhang, M.

(2013) Proc Natl Acad Sci U S A 110: 11314-11319

  • DOI: https://doi.org/10.1073/pnas.1306768110
  • Primary Citation Related Structures: 
    3WB8, 4KP3

  • PubMed Abstract: 

    Class V myosins (MyoV), the most studied unconventional myosins, recognize numerous cargos mainly via the motor's globular tail domain (GTD). Little is known regarding how MyoV-GTD recognizes such a diverse array of cargos specifically. Here, we solved the crystal structures of MyoVa-GTD in its apo-form and in complex with two distinct cargos, melanophilin and Rab interacting lysosomal protein-like 2. The apo-MyoVa-GTD structure indicates that most mutations found in patients with Griscelli syndrome, microvillus inclusion disease, or cancers or in "dilute" rodents likely impair the folding of GTD. The MyoVa-GTD/cargo complex structure reveals two distinct cargo-binding surfaces, one primarily via charge-charge interaction and the other mainly via hydrophobic interactions. Structural and biochemical analysis reveal the specific cargo-binding specificities of various isoforms of mammalian MyoV as well as very different cargo recognition mechanisms of MyoV between yeast and higher eukaryotes. The MyoVa-GTD structures resolved here provide a framework for future functional studies of vertebrate class V myosins.


  • Organizational Affiliation
    • Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.

Macromolecule Content 

  • Total Structure Weight: 125.19 kDa 
  • Atom Count: 7,359 
  • Modeled Residue Count: 907 
  • Deposited Residue Count: 1,100 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Unconventional myosin-VaA,
D [auth B]
404Mus musculusMutation(s): 1 
Gene Names: Myo5a
UniProt & NIH Common Fund Data Resources
Find proteins for Q99104 (Mus musculus)
Explore Q99104 
Go to UniProtKB:  Q99104
IMPC:  MGI:105976
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99104
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RILP-like protein 2B [auth C],
E [auth D]
103Mus musculusMutation(s): 0 
Gene Names: Rilpl2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99LE1 (Mus musculus)
Explore Q99LE1 
Go to UniProtKB:  Q99LE1
IMPC:  MGI:1933112
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99LE1
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MelanophilinC [auth E],
F
43Mus musculusMutation(s): 0 
Gene Names: Mlph
UniProt
Find proteins for Q91V27 (Mus musculus)
Explore Q91V27 
Go to UniProtKB:  Q91V27
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91V27
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.241 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.85α = 90
b = 107.933β = 96.14
c = 83.51γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description