Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.63 kDa 
• Atom Count: 3,181 
• Modelled Residue Count: 363 
• Deposited Residue Count: 396 
• Unique protein chains: 1

 4J5M

Structure of the Cargo Binding Domain from Human Myosin Vb

• PDB DOI:  https://doi.org/10.2210/pdb4J5M/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-02-08 Released: 2013-10-09 
• Deposition Author(s): Nascimento, A.F.Z., Trindade, D.M., Mahajan, P., Berridge, G., Krojer, T., Vollmar, M., Tonoli, C.C.C., Assis, L.H.P., Burgess-Brown, N., von Delft, F., Murakami, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Structural Insights into Functional Overlapping and Differentiation among Myosin V Motors.

Nascimento, A.F., Trindade, D.M., Tonoli, C.C., de Giuseppe, P.O., Assis, L.H., Honorato, R.V., de Oliveira, P.S., Mahajan, P., Burgess-Brown, N.A., von Delft, F., Larson, R.E., Murakami, M.T.

(2013) J Biol Chem 288: 34131-34145

• PubMed: 24097982 
• DOI: https://doi.org/10.1074/jbc.M113.507202
• Primary Citation of Related Structures:  
  4J5L, 4J5M, 4L8T


• PubMed Abstract: 
  

Myosin V (MyoV) motors have been implicated in the intracellular transport of diverse cargoes including vesicles, organelles, RNA-protein complexes, and regulatory proteins. Here, we have solved the cargo-binding domain (CBD) structures of the three human MyoV paralogs (Va, Vb, and Vc), revealing subtle structural changes that drive functional differentiation and a novel redox mechanism controlling the CBD dimerization process, which is unique for the MyoVc subclass. Moreover, the cargo- and motor-binding sites were structurally assigned, indicating the conservation of residues involved in the recognition of adaptors for peroxisome transport and providing high resolution insights into motor domain inhibition by CBD. These results contribute to understanding the structural requirements for cargo transport, autoinhibition, and regulatory mechanisms in myosin V motors.

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Organizational Affiliation: 

Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-100, Brazil. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unconventional myosin-Vb	A	396	Homo sapiens	Mutation(s): 0  Gene Names: KIAA1119, MYO5B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULV0 (Homo sapiens) Explore Q9ULV0  Go to UniProtKB:  Q9ULV0
PHAROS:  Q9ULV0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	B [auth A], C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.093	α = 90
b = 78.2	β = 90
c = 151.817	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
Rosetta	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Nascimento, A.F.Z., Trindade, D.M., Mahajan, P., Berridge, G., Krojer, T., Vollmar, M., Tonoli, C.C.C., Assis, L.H.P., Burgess-Brown, N., von Delft, F., Murakami, M.T.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2013-12-11
  Changes: Database references