9RFB | pdb_00009rfb

Crystal Structure of Human Rac1 in Complex with the Scaffold Protein POSH (residues 321-348)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.226 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.202 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Hierarchical folding-upon-binding of an intrinsically disordered protein.

Kjaer, L.F.Ielasi, F.S.Winbolt, T.Delaforge, E.Tengo, M.Bessa, L.M.Marino Perez, L.Boeri Erba, E.Bouvignies, G.Palencia, A.Jensen, M.R.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-66420-5
  • Primary Citation of Related Structures:  
    9RFB, 9RFF

  • PubMed Abstract: 

    Intrinsically disordered proteins (IDPs) often undergo folding-upon-binding to their partners via short linear motifs, typically 5-15 amino acids in length. However, a significant proportion of IDPs do not adhere to this paradigm but fold upon binding through extended regions comprising multiple molecular recognition elements. For these IDPs, the binding mechanisms and the structural characteristics of their folding intermediates remain poorly understood. Here we unveil hierarchical folding of an IDP as it binds to its partner, exemplified by the disordered signaling effector POSH and the small GTPase Rac1. By combining nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, we resolve at atomic resolution how POSH transitions from a fully disordered state to a highly ordered, Rac1-bound conformation through two structurally distinct folding intermediates. The folding of each element is contingent on the successful structuring of the preceding element, highlighting a hierarchical folding-upon-binding mechanism. Our work highlights the potential of targeting folding intermediates and conformational transitions to unlock therapeutic opportunities for IDPs.


  • Organizational Affiliation
    • Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1
A, B
180Homo sapiensMutation(s): 0 
Gene Names: RAC1TC25MIG5
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens)
Explore P63000 
Go to UniProtKB:  P63000
PHAROS:  P63000
GTEx:  ENSG00000136238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63000
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase SH3RF1
C, D
28Homo sapiensMutation(s): 0 
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6J0 (Homo sapiens)
Explore Q7Z6J0 
Go to UniProtKB:  Q7Z6J0
PHAROS:  Q7Z6J0
GTEx:  ENSG00000154447 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z6J0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.226 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.793α = 90
b = 54.793β = 90
c = 329.942γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-21-CE11-0033
Agence Nationale de la Recherche (ANR)FranceANR-10-INBS-0005-02
Agence Nationale de la Recherche (ANR)FranceANR-17-EURE-0003
European Union (EU)European UnionHORIZON-MSCA-2022-DN-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references