6OA6

CRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF HUMAN ALPHA-ACTININ-4

• PDB DOI: https://doi.org/10.2210/pdb6OA6/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-03-15 Released: 2020-03-18 
• Deposition Author(s): Birrane, G., Feng, D.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.172 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 

Literature

Phosphorylation of ACTN4 Leads to Podocyte Vulnerability and Proteinuric Glomerulosclerosis.

Feng, D., Kumar, M., Muntel, J., Gurley, S.B., Birrane, G., Stillman, I.E., Ding, L., Wang, M., Ahmed, S., Schlondorff, J., Alper, S.L., Ferrante, T., Marquez, S.L., Ng, C.F., Novak, R., Ingber, D.E., Steen, H., Pollak, M.R.

(2020) J Am Soc Nephrol 31: 1479-1495

• PubMed: 32540856 
• DOI: https://doi.org/10.1681/ASN.2019101032
• Primary Citation of Related Structures:  
  6O31, 6OA6


• PubMed Abstract: 
  

  Genetic mutations in α -actinin-4 (ACTN4)-an important actin crosslinking cytoskeletal protein that provides structural support for kidney podocytes-have been linked to proteinuric glomerulosclerosis in humans. However, the effect of post-translational modifications of ACTN4 on podocyte integrity and kidney function is not known.

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Organizational Affiliation: 

Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts [e-mail] [e-mail].

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: 26.83 kDa 
• Atom Count: 2,240 
• Modelled Residue Count: 227 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-actinin-4	A	234	Homo sapiens	Mutation(s): 1  Gene Names: ACTN4
UniProt & NIH Common Fund Data Resources
Find proteins for O43707 (Homo sapiens) Explore O43707  Go to UniProtKB:  O43707
PHAROS:  O43707 GTEx:  ENSG00000130402

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.172 
• R-Value Work: 0.134 
• R-Value Observed: 0.136 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.589	α = 90
b = 61.732	β = 90
c = 89.534	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Birrane, G., Feng, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK59588
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK114329
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK007199

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-09-09
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description