3ERR

Microtubule binding domain from mouse cytoplasmic dynein as a fusion with seryl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb3ERR/pdb

• Classification: LIGASE
• Organism(s): Mus musculus, Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-03 Released: 2008-11-25 
• Deposition Author(s): Carter, A.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.247 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Structure and functional role of dynein's microtubule-binding domain.

Carter, A.P., Garbarino, J.E., Wilson-Kubalek, E.M., Shipley, W.E., Cho, C., Milligan, R.A., Vale, R.D., Gibbons, I.R.

(2008) Science 322: 1691-1695

• PubMed: 19074350 
• DOI: https://doi.org/10.1126/science.1164424
• Primary Citation of Related Structures:  
  3ERR


• PubMed Abstract: 
  

  Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 122.61 kDa 
• Atom Count: 8,589 
• Modelled Residue Count: 1,054 
• Deposited Residue Count: 1,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fusion protein of microtubule binding domain from mouse cytoplasmic dynein and seryl-tRNA synthetase from Thermus thermophilus	A, B	536	Mus musculus, Thermus thermophilus HB27 This entity is chimeric	Mutation(s): 2  EC: 6.1.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SJX7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJX7  Go to UniProtKB:  Q5SJX7
Find proteins for Q9JHU4 (Mus musculus) Explore Q9JHU4  Go to UniProtKB:  Q9JHU4
IMPC:  MGI:103147
UniProt Groups	Q9JHU4Q5SJX7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.247 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.302	α = 90
b = 144.302	β = 90
c = 159.946	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Carter, A.P.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2021-10-20
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description