7ZAU

Fascin-1 in complex with Nb 3E11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A nanobody inhibitor of Fascin-1 actin-bundling activity and filopodia formation.

Burgess, S.G.Paul, N.R.Richards, M.W.Ault, J.R.Askenatzis, L.Claydon, S.G.Corbyn, R.Machesky, L.M.Bayliss, R.

(2024) Open Biol 14: 230376-230376

  • DOI: https://doi.org/10.1098/rsob.230376
  • Primary Citation of Related Structures:  
    7ZAU

  • PubMed Abstract: 

    Fascin-1-mediated actin-bundling activity is central to the generation of plasma membrane protrusions required for cell migration. Dysregulated formation of cellular protrusions is observed in metastatic cancers, where they are required for increased invasiveness, and is often correlated with increased Fascin-1 abundance. Therefore, there is interest in generating therapeutic Fascin-1 inhibitors. We present the identification of Nb 3E11, a nanobody inhibitor of Fascin-1 actin-bundling activity and filopodia formation. The crystal structure of the Fascin-1/Nb 3E11 complex reveals the structural mechanism of inhibition. Nb 3E11 occludes an actin-binding site on the third β-trefoil domain of Fascin-1 that is currently not targeted by chemical inhibitors. Binding of Nb 3E11 to Fascin-1 induces a conformational change in the adjacent domains to stabilize Fascin-1 in an inhibitory state similar to that adopted in the presence of small-molecule inhibitors. Nb 3E11 could be used as a tool inhibitor molecule to aid in the development of Fascin-1 targeted therapeutics.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fascin
A, C, E, G
498Homo sapiensMutation(s): 0 
Gene Names: FSCN1FAN1HSNSNL
UniProt & NIH Common Fund Data Resources
Find proteins for Q16658 (Homo sapiens)
Explore Q16658 
Go to UniProtKB:  Q16658
PHAROS:  Q16658
GTEx:  ENSG00000075618 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16658
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 3E11
B, D, F, H
132Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth G],
Q [auth C],
R [auth E],
S [auth E],
T [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
I [auth A]
J [auth A]
K [auth A]
AA [auth G],
CA [auth H],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth C],
P [auth C],
U [auth E],
V [auth E],
W [auth E],
X [auth E],
Y [auth E],
Z [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.907α = 90
b = 210.324β = 91.262
c = 105.469γ = 90
Software Package:
Software NamePurpose
DIALSdata scaling
DIALSdata reduction
MOLREPphasing
Zanudadata reduction
PHENIXrefinement
Cootmodel building
MolProbitymodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC24461/A23303

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary