3L9K | pdb_00003l9k

Insights into dynein assembly from a dynein intermediate chain-light chain roadblock structure

• PDB DOI: https://doi.org/10.2210/pdb3L9K/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-05 Released: 2010-05-12 
• Deposition Author(s): Hall, J., Karplus, P.A., Barbar, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Insights into dynein assembly from a dynein intermediate chain-light chain roadblock structure

Hall, J., Karplus, P.A., Barbar, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.3 kDa 
• Atom Count: 4,180 
• Modeled Residue Count: 532 
• Deposited Residue Count: 540 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RE64145p	A, B, C, D	97	Drosophila melanogaster	Mutation(s): 0  Gene Names: robl, CG10751, Dmel_CG10751
UniProt
Find proteins for Q7KMS3 (Drosophila melanogaster) Explore Q7KMS3  Go to UniProtKB:  Q7KMS3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein intermediate chain, cytosolic	E [auth W], F [auth X], G [auth Y], H [auth Z]	38	Drosophila melanogaster	Mutation(s): 0  Gene Names: sw, Cdic, Dic19B, CG18000
UniProt
Find proteins for Q24246 (Drosophila melanogaster) Explore Q24246  Go to UniProtKB:  Q24246

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.18	α = 90
b = 107.18	β = 90
c = 65.41	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Hall, J., Karplus, P.A., Barbar, E.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-09-18
  Changes: Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description