9RFB | pdb_00009rfb

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

PDB DOI: https://doi.org/10.2210/pdb9RFB/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-04 Released: 2025-12-03
Deposition Author(s): Kjaer, L.F., Ielasi, F.S., Palencia, A., Jensen, M.R.
Funding Organization(s): Agence Nationale de la Recherche (ANR), European Union (EU)

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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

Macromolecule Content

Total Structure Weight: 47.46 kDa
Atom Count: 3,571
Modeled Residue Count: 400
Deposited Residue Count: 416
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	A, B	180	Homo sapiens	Mutation(s): 0 Gene Names: RAC1, TC25, MIG5 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63000
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase SH3RF1	C, D	28	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z6J0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP (Subject of Investigation/LOI) Query on GNP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

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)

Diffraction Data: https://doi.org/10.15151/ESRF-ES-879283716

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.793	α = 90
b = 54.793	β = 90
c = 329.942	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-21-CE11-0033
Agence Nationale de la Recherche (ANR)	France	ANR-10-INBS-0005-02
Agence Nationale de la Recherche (ANR)	France	ANR-17-EURE-0003
European Union (EU)	European Union	HORIZON-MSCA-2022-DN-01

Revision History (Full details and data files)

Version 1.0: 2025-12-03
Type: Initial release

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

Hierarchical Folding-Upon-Binding of an Intrinsically Disordered Protein

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2