7C2F | pdb_00007c2f

Crystal Structure of the Thorarchaeota ProGel/rabbit actin complex

• PDB DOI: https://doi.org/10.2210/pdb7C2F/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Oryctolagus cuniculus, Candidatus Thorarchaeota archaeon SMTZ1-83
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-07 Released: 2020-08-05 
• Deposition Author(s): Robinson, R.C., Akil, C.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Insights into the evolution of regulated actin dynamics via characterization of primitive gelsolin/cofilin proteins from Asgard archaea

Akil, C., Tran, L.T., Orhant-Prioux, M., Baskaran, Y., Manser, E., Blanchoin, L., Robinson, R.C.

(2020) Proc Natl Acad Sci U S A 117: 19904-19913

• DOI: https://doi.org/10.1073/pnas.2009167117

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 106.89 kDa 
• Atom Count: 7,817 
• Modeled Residue Count: 899 
• Deposited Residue Count: 938 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, C	375	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gelsolin-like domain-containing protein	B, D	94	Candidatus Thorarchaeota archaeon SMTZ1-83	Mutation(s): 0
UniProt
Find proteins for A0ACD6B9Y8 (Candidatus Thorarchaeota archaeon SMTZ1-83) Explore A0ACD6B9Y8  Go to UniProtKB:  A0ACD6B9Y8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	F [auth A], I [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
LAB	E [auth A], H [auth C]	LATRUNCULIN B C20 H29 N O5 S NSHPHXHGRHSMIK-JRIKCGFMSA-N
MG	G [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A, C	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.427	α = 90
b = 108.626	β = 90
c = 167.522	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Robinson, R.C., Akil, C.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H00476

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Database references, Structure summary
• Version 1.2: 2023-01-04
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description