7SHL

Structure of Xenopus laevis CRL2Lrr1 (State 2)

  • Classification: LIGASE
  • Organism(s): Xenopus laevis
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2021-10-09 Released: 2021-12-08 
  • Deposition Author(s): Zhou, H., Brown, A.
  • Funding Organization(s): Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates.

Zhou, H.Zaher, M.S.Walter, J.C.Brown, A.

(2021) Nucleic Acids Res 49: 13194-13206

  • DOI: https://doi.org/10.1093/nar/gkab1174
  • Primary Citation of Related Structures:  
    7SHK, 7SHL

  • PubMed Abstract: 

    When vertebrate replisomes from neighboring origins converge, the Mcm7 subunit of the replicative helicase, CMG, is ubiquitylated by the E3 ubiquitin ligase, CRL2Lrr1. Polyubiquitylated CMG is then disassembled by the p97 ATPase, leading to replication termination. To avoid premature replisome disassembly, CRL2Lrr1 is only recruited to CMGs after they converge, but the underlying mechanism is unclear. Here, we use cryogenic electron microscopy to determine structures of recombinant Xenopus laevis CRL2Lrr1 with and without neddylation. The structures reveal that CRL2Lrr1 adopts an unusually open architecture, in which the putative substrate-recognition subunit, Lrr1, is located far from the catalytic module that catalyzes ubiquitin transfer. We further demonstrate that a predicted, flexible pleckstrin homology domain at the N-terminus of Lrr1 is essential to target CRL2Lrr1 to terminated CMGs. We propose a hypothetical model that explains how CRL2Lrr1's catalytic module is positioned next to the ubiquitylation site on Mcm7, and why CRL2Lrr1 binds CMG only after replisomes converge.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CULLIN_2 domain-containing protein745Xenopus laevisMutation(s): 0 
Gene Names: cul2.Lcul2XELAEV_18030721mg
UniProt
Find proteins for Q6PCF2 (Xenopus laevis)
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Go to UniProtKB:  Q6PCF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PCF2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tceb2-prov protein119Xenopus laevisMutation(s): 0 
Gene Names: elob.Lelobtceb2
UniProt
Find proteins for Q6PHL7 (Xenopus laevis)
Explore Q6PHL7 
Go to UniProtKB:  Q6PHL7
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UniProt GroupQ6PHL7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C112Xenopus laevisMutation(s): 0 
Gene Names: eloc.Leloctceb1XELAEV_18031836mgXELAEV_18033803mg
UniProt
Find proteins for Q6PHW7 (Xenopus laevis)
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Go to UniProtKB:  Q6PHW7
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UniProt GroupQ6PHW7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Lrr1D [auth L]418Xenopus laevisMutation(s): 0 
Gene Names: lrr1.Llrr1MGC82386XELAEV_18039633mg
UniProt
Find proteins for A4QNS4 (Xenopus laevis)
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UniProt GroupA4QNS4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RING-type domain-containing proteinE [auth R]108Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18023559mg
UniProt
Find proteins for A0A1L8GNJ6 (Xenopus laevis)
Explore A0A1L8GNJ6 
Go to UniProtKB:  A0A1L8GNJ6
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UniProt GroupA0A1L8GNJ6
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth L]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM141109
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM80676

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references