7C2H | pdb_00007c2h

Crystal Structure of the Thorarchaeota 2DGel3/rabbit actin complex

• PDB DOI: https://doi.org/10.2210/pdb7C2H/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.238 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (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 and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 65.9 kDa 
• Atom Count: 4,599 
• Modeled Residue Count: 553 
• Deposited Residue Count: 577 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	377	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
2DGel3	B [auth G]	200	Candidatus Thorarchaeota archaeon SMTZ1-83	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	C [auth A], E [auth G], F [auth G], G, H [auth G], I [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.238 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.915	α = 90
b = 98.644	β = 94.02
c = 62.448	γ = 90

Software Package:

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

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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