6ZEE

Structure of PP1(7-300) bound to Phactr1 (507-580) at pH8.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme.

Fedoryshchak, R.O.Prechova, M.Butler, A.Lee, R.O'Reilly, N.Flynn, H.R.Snijders, A.P.Eder, N.Ultanir, S.Mouilleron, S.Treisman, R.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.61509
  • Primary Citation of Related Structures:  
    6ZEE, 6ZEF, 6ZEG, 6ZEH, 6ZEI, 6ZEJ

  • PubMed Abstract: 

    PPP-family phosphatases such as PP1 have little intrinsic specificity. Cofactors can target PP1 to substrates or subcellular locations, but it remains unclear how they might confer sequence-specificity on PP1. The cytoskeletal regulator Phactr1 is a neuronally enriched PP1 cofactor that is controlled by G-actin. Structural analysis showed that Phactr1 binding remodels PP1's hydrophobic groove, creating a new composite surface adjacent to the catalytic site. Using phosphoproteomics, we identified mouse fibroblast and neuronal Phactr1/PP1 substrates, which include cytoskeletal components and regulators. We determined high-resolution structures of Phactr1/PP1 bound to the dephosphorylated forms of its substrates IRSp53 and spectrin αII. Inversion of the phosphate in these holoenzyme-product complexes supports the proposed PPP-family catalytic mechanism. Substrate sequences C-terminal to the dephosphorylation site make intimate contacts with the composite Phactr1/PP1 surface, which are required for efficient dephosphorylation. Sequence specificity explains why Phactr1/PP1 exhibits orders-of-magnitude enhanced reactivity towards its substrates, compared to apo-PP1 or other PP1 holoenzymes.


  • Organizational Affiliation

    Signalling and Transcription Laboratory, The Francis Crick Institute, London, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit299Homo sapiensMutation(s): 0 
Gene Names: PPP1CAPPP1A
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P62136 (Homo sapiens)
Explore P62136 
Go to UniProtKB:  P62136
GTEx:  ENSG00000172531 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62136
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatase and actin regulator78Homo sapiensMutation(s): 0 
Gene Names: PHACTR1hCG_1818446
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0D0 (Homo sapiens)
Explore Q9C0D0 
Go to UniProtKB:  Q9C0D0
GTEx:  ENSG00000112137 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C0D0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
16P (Subject of Investigation/LOI)
Query on 16P

Download Ideal Coordinates CCD File 
GB [auth A]3,6,9,12,15,18-HEXAOXAICOSANE
C14 H30 O6
IXFAFGFZFQHRLB-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
GA [auth Q]
JC [auth K]
KC [auth W]
OC [auth D]
PB [auth A]
GA [auth Q],
JC [auth K],
KC [auth W],
OC [auth D],
PB [auth A],
QC [auth C],
SC [auth U],
UB [auth I],
UC [auth V],
VB [auth I],
WA [auth B],
X [auth P],
XA [auth B],
Y [auth P]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EC [auth K]
IC [auth K]
LC [auth X]
MC [auth D]
PC [auth C]
EC [auth K],
IC [auth K],
LC [auth X],
MC [auth D],
PC [auth C],
U [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth I]
BA [auth Q]
BB [auth A]
CA [auth Q]
AB [auth A],
AC [auth I],
BA [auth Q],
BB [auth A],
CA [auth Q],
CB [auth A],
DA [auth Q],
DB [auth A],
DC [auth K],
EA [auth Q],
EB [auth A],
FA [auth Q],
FB [auth A],
FC [auth K],
GC [auth K],
HB [auth A],
HC [auth K],
IB [auth A],
JA [auth B],
JB [auth A],
KA [auth B],
KB [auth A],
LA [auth B],
LB [auth A],
MA [auth B],
MB [auth A],
NA [auth B],
NB [auth A],
NC [auth D],
O [auth P],
OA [auth B],
OB [auth A],
P,
PA [auth B],
Q [auth P],
QA [auth B],
R [auth P],
RA [auth B],
RC [auth U],
S [auth P],
SA [auth B],
SB [auth I],
T [auth P],
TA [auth B],
TB [auth I],
TC [auth V],
UA [auth B],
V [auth P],
VA [auth B],
W [auth P],
WB [auth I],
XB [auth I],
YB [auth I],
ZB [auth I]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth Q]
BC [auth K]
CC [auth K]
HA [auth B]
IA [auth B]
AA [auth Q],
BC [auth K],
CC [auth K],
HA [auth B],
IA [auth B],
M [auth P],
N [auth P],
QB [auth I],
RB [auth I],
YA [auth A],
Z [auth Q],
ZA [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.695α = 90
b = 137.695β = 90
c = 238.793γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description