5YXM | pdb_00005yxm

Crystal structure of Chlamydomonas Outer Arm Dynein Light Chain 1

• PDB DOI: https://doi.org/10.2210/pdb5YXM/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-06 Released: 2018-03-14 
• Deposition Author(s): Toda, A., Tanaka, H., Nishikawa, Y., Yagi, T., Kurisu, G.
• Funding Organization(s): Grant-in-Aid for JSPS Fellows, Grant-in-Aid for Scientific Research(B)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Models: experimental

Literature

Structural atlas of dynein motors at atomic resolution.

Toda, A., Tanaka, H., Kurisu, G.

(2018) Biophys Rev 10: 677-686

• PubMed: 29478092 
• DOI: https://doi.org/10.1007/s12551-018-0402-y
• Primary Citation Related Structures: 
  5YXM


• PubMed Abstract: 
  

  Dynein motors are biologically important bio-nanomachines, and many atomic resolution structures of cytoplasmic dynein components from different organisms have been analyzed by X-ray crystallography, cryo-EM, and NMR spectroscopy. This review provides a historical perspective of structural studies of cytoplasmic and axonemal dynein including accessory proteins. We describe representative structural studies of every component of dynein and summarize them as a structural atlas that classifies the cytoplasmic and axonemal dyneins. Based on our review of all dynein structures in the Protein Data Bank, we raise two important points for understanding the two types of dynein motor and discuss the potential prospects of future structural studies.

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Organizational Affiliation: 
• Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.88 kDa 
• Atom Count: 1,825 
• Modeled Residue Count: 194 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain 1, axonemal	A	203	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: LC1, CHLREDRAFT_186669
UniProt
Find proteins for Q9XHH2 (Chlamydomonas reinhardtii) Explore Q9XHH2  Go to UniProtKB:  Q9XHH2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.536	α = 90
b = 69.23	β = 90
c = 74.775	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
BALBES	phasing
Coot	model building
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Toda, A., Tanaka, H., Nishikawa, Y., Yagi, T., Kurisu, G.

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Funding Organization	Location	Grant Number
Grant-in-Aid for JSPS Fellows	Japan	17J075530
Grant-in-Aid for Scientific Research(B)	Japan	26291014

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-04-25
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description