5WFN | pdb_00005wfn

Revised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4RWT)

• PDB DOI: https://doi.org/10.2210/pdb5WFN/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Drosophila melanogaster, Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-07-12 Released: 2017-08-30 
• Deposition Author(s): Yurtsever, Z., Eck, M.J., Dominguez, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4RWT

Literature

Crystal structure of leiomodin 2 in complex with actin: a structural and functional reexamination

Boczkowska, M., Yurtsever, Z., Rebowski, G., Eck, M.J., Dominguez, R.

(2017) Biophys J 113: 889-899

• DOI: https://doi.org/10.1016/j.bpj.2017.07.007

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 Evidence: isothermal titration calorimetry, assay for oligomerization

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 200.34 kDa 
• Atom Count: 8,906 
• Modeled Residue Count: 1,126 
• Deposited Residue Count: 1,780 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-5C	A, C [auth B]	384	Drosophila melanogaster	Mutation(s): 2  Gene Names: Act5C, CG4027 EC: 3.6.4
UniProt
Find proteins for P10987 (Drosophila melanogaster) Explore P10987  Go to UniProtKB:  P10987

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leiomodin-2	B [auth C], D	506	Homo sapiens	Mutation(s): 8  Gene Names: LMOD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P5Q4 (Homo sapiens) Explore Q6P5Q4  Go to UniProtKB:  Q6P5Q4
PHAROS:  Q6P5Q4 GTEx:  ENSG00000170807

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	E [auth A], G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.35	α = 101.29
b = 65.65	β = 90.94
c = 81.92	γ = 107.97

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Yurtsever, Z., Eck, M.J., Dominguez, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM073791
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM110352

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2018-01-31
  Changes: Database references
• Version 1.3: 2018-08-22
  Changes: Data collection, Database references
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 1.5: 2020-09-23
  Changes: Database references, Derived calculations
• Version 1.6: 2024-03-13
  Changes: Data collection, Database references