7RNU | pdb_00007rnu

nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an actin peptide with phosphorylated tyrosine 53

• PDB DOI: https://doi.org/10.2210/pdb7RNU/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-29 Released: 2021-08-11 
• Deposition Author(s): Dai, S., Horton, J.R., Cheng, X.
• 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: 1.45 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

The Functional Analysis of a Major Tyrosine Phosphorylation Site on Actin

Amelie, A., Dai, S., Shen, X., Horton, J.R., Zhang, X., Cheng, X.

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.87 kDa 
• Atom Count: 4,196 
• Modeled Residue Count: 461 
• Deposited Residue Count: 492 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit beta	A, C, E, G	114	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R2
UniProt & NIH Common Fund Data Resources
Find proteins for O00459 (Homo sapiens) Explore O00459  Go to UniProtKB:  O00459
PHAROS:  O00459 GTEx:  ENSG00000105647

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	B, D, F, H	9	Homo sapiens	Mutation(s): 0  EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P68133 (Homo sapiens) Explore P68133  Go to UniProtKB:  P68133
PHAROS:  P68133 GTEx:  ENSG00000143632

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], J [auth A], K [auth A], L [auth C], M [auth C], N [auth C], O [auth G], P [auth G]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B, D, F, H	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.083	α = 90
b = 41.432	β = 100.294
c = 65.875	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Dai, S., Horton, J.R., Cheng, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM049245-23

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-13
  Changes: Structure summary