8A9K

Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site.

Rennie, M.L.Arkinson, C.Chaugule, V.K.Walden, H.

(2022) Sci Adv 8: eabq6353-eabq6353

  • DOI: https://doi.org/10.1126/sciadv.abq6353
  • Primary Citation of Related Structures:  
    7ZH3, 7ZH4, 8A9J, 8A9K

  • PubMed Abstract: 

    Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. Ubiquitin-specific protease 1 (USP1), a nucleus-localized deubiquitinase, lies at the interface of multiple DNA repair pathways and is a promising drug target for certain cancers. Although multiple inhibitors of this enzyme, including one in phase 1 clinical trials, have been established, their binding mode is unknown. Here, we use cryo-electron microscopy to study an assembled enzyme-substrate-inhibitor complex of USP1 and the well-established inhibitor, ML323. Achieving 2.5-Å resolution, with and without ML323, we find an unusual binding mode in which the inhibitor disrupts part of the hydrophobic core of USP1. The consequent conformational changes in the secondary structure lead to subtle rearrangements in the active site that underlie the mechanism of inhibition. These structures provide a platform for structure-based drug design targeting USP1.


  • Organizational Affiliation

    Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fanconi anemia group I protein1,335Homo sapiensMutation(s): 0 
Gene Names: FANCIKIAA1794
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVI1 (Homo sapiens)
Explore Q9NVI1 
Go to UniProtKB:  Q9NVI1
PHAROS:  Q9NVI1
GTEx:  ENSG00000140525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVI1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fanconi anemia group D2 protein1,455Homo sapiensMutation(s): 0 
Gene Names: FANCD2FACD
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXW9 (Homo sapiens)
Explore Q9BXW9 
Go to UniProtKB:  Q9BXW9
PHAROS:  Q9BXW9
GTEx:  ENSG00000144554 
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UniProt GroupQ9BXW9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-C80Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 1786Homo sapiensMutation(s): 3 
Gene Names: USP1
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O94782 (Homo sapiens)
Explore O94782 
Go to UniProtKB:  O94782
PHAROS:  O94782
GTEx:  ENSG00000162607 
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UniProt GroupO94782
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 48694Homo sapiensMutation(s): 0 
Gene Names: WDR48KIAA1449UAF1
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Find proteins for Q8TAF3 (Homo sapiens)
Explore Q8TAF3 
Go to UniProtKB:  Q8TAF3
PHAROS:  Q8TAF3
GTEx:  ENSG00000114742 
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UniProt GroupQ8TAF3
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (61-MER)F [auth S],
G [auth T]
29synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JDA (Subject of Investigation/LOI)
Query on JDA

Download Ideal Coordinates CCD File 
I [auth D]5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine
C23 H24 N6
VUIRVWPJNKZOSS-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JDA BindingDB:  8A9K IC50: min: 17, max: 190 (nM) from 6 assay(s)
EC50: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.19

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2015-CoG-681582
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_12016/12

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 2.0: 2023-03-01
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary