7AJK | pdb_00007ajk

Crystal structure of CRYI-B Rac1 complex

• PDB DOI: https://doi.org/10.2210/pdb7AJK/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-29 Released: 2020-11-18 
• Deposition Author(s): Yelland, T., Anh, L., Insall, R., Machesky, L., Ismail, S.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.282 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.251 (DCC) 

Starting Model: experimental

Literature

Structural Basis of CYRI-B Direct Competition with Scar/WAVE Complex for Rac1.

Yelland, T., Le, A.H., Nikolaou, S., Insall, R., Machesky, L., Ismail, S.

(2021) Structure 29: 226-237.e4

• PubMed: 33217330 
• DOI: https://doi.org/10.1016/j.str.2020.11.003
• Primary Citation Related Structures: 
  7AJK, 7AJL


• PubMed Abstract: 
  

  Rac1 is a major regulator of actin dynamics, with GTP-bound Rac1 promoting actin assembly via the Scar/WAVE complex. CYRI competes with Scar/WAVE for interaction with Rac1 in a feedback loop regulating actin dynamics. Here, we reveal the nature of the CYRI-Rac1 interaction, through crystal structures of CYRI-B lacking the N-terminal helix (CYRI-BΔN) and the CYRI-BΔN:Rac1Q61L complex, providing the molecular basis for CYRI-B regulation of the Scar/WAVE complex. We reveal CYRI-B as having two subdomains - an N-terminal Rac1 binding subdomain with a unique Rac1-effector interface and a C-terminal Ratchet subdomain that undergoes conformational changes induced by Rac1 binding. Finally, we show that the CYRI protein family, CYRI-A and CYRI-B can produce an autoinhibited hetero- or homodimers, adding an additional layer of regulation to Rac1 signaling.

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Organizational Affiliation: 
• CRUK- Beatson Institute, Glasgow G61 1BD, UK.
CRUK- Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK.
CRUK- Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK. Electronic address: [e-mail].
CRUK- Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK; Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium. Electronic address: [e-mail].

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 Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 57.23 kDa 
• Atom Count: 3,612 
• Modeled Residue Count: 456 
• Deposited Residue Count: 505 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	A [auth BBB]	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYFIP-related Rac1 interactor B	B [auth CCC]	325	Homo sapiens	Mutation(s): 0  Gene Names: CYRIB, CYRI, FAM49B, BM-009
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUQ9 (Homo sapiens) Explore Q9NUQ9  Go to UniProtKB:  Q9NUQ9
PHAROS:  Q9NUQ9 GTEx:  ENSG00000153310

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	D [auth BBB]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	C [auth BBB]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.282 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.251 (DCC) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.87	α = 90
b = 81.87	β = 90
c = 355.87	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Yelland, T., Anh, L., Insall, R., Machesky, L., Ismail, S.

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Funding Organization	Location	Grant Number
Cancer Research UK		--

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-06-02
  Changes: Data collection, Database references
• Version 1.2: 2024-01-31
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description