6JH8 | pdb_00006jh8

Crystal structure of an actin monomer in complex with a chimeric peptide of Cordon-Bleu WH2 mutant and MIM.

• PDB DOI: https://doi.org/10.2210/pdb6JH8/pdb

• Classification: STRUCTURAL PROTEIN/PROTEIN BINDING
• Organism(s): Oryctolagus cuniculus, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-17 Released: 2020-02-19 
• Deposition Author(s): Scipion, C.P.M., Robinson, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Design of an actin-severing peptide.

Scipion, C.P.M., Robinson, R.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.89 kDa 
• Atom Count: 3,318 
• Modeled Residue Count: 390 
• Deposited Residue Count: 406 
• 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
Cordon-Bleu MIM chimeric peptide	B	29	Mus musculus	Mutation(s): 0  Gene Names: Cobl, Kiaa0633
UniProt & NIH Common Fund Data Resources
Find proteins for Q5NBX1 (Mus musculus) Explore Q5NBX1  Go to UniProtKB:  Q5NBX1
IMPC:  MGI:105056

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	D [auth A], E [auth A]	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: 2.15 Å
• R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.439	α = 90
b = 56.073	β = 93.4
c = 38.432	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Scipion, C.P.M., Robinson, R.C.

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description