6KTO

Crystal structure of human SHLD3-C-REV7-O-REV7-SHLD2 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Molecular basis for assembly of the shieldin complex and its implications for NHEJ.

Liang, L., Feng, J., Zuo, P., Yang, J., Lu, Y., Yin, Y.

(2020) Nat Commun 11: 1972-1972

  • DOI: 10.1038/s41467-020-15879-5
  • Primary Citation of Related Structures:  
    6KTO

  • PubMed Abstract: 

    • Shieldin, including SHLD1, SHLD2, SHLD3 and REV7, functions as a bridge linking 53BP1-RIF1 and single-strand DNA to suppress the DNA termini nucleolytic resection during non-homologous end joining (NHEJ). However, the mechanism of shieldin assembly remains unclear ...

    Shieldin, including SHLD1, SHLD2, SHLD3 and REV7, functions as a bridge linking 53BP1-RIF1 and single-strand DNA to suppress the DNA termini nucleolytic resection during non-homologous end joining (NHEJ). However, the mechanism of shieldin assembly remains unclear. Here we present the crystal structure of the SHLD3-REV7-SHLD2 ternary complex and reveal an unexpected C (closed)-REV7-O (open)-REV7 conformational dimer mediated by SHLD3. We show that SHLD2 interacts with O-REV7 and the N-terminus of SHLD3 by forming β sheet sandwich. Disruption of the REV7 conformational dimer abolishes the assembly of shieldin and impairs NHEJ efficiency. The conserved FXPWFP motif of SHLD3 binds to C-REV7 and blocks its binding to REV1, which excludes shieldin from the REV1/Pol ζ translesion synthesis (TLS) complex. Our study reveals the molecular architecture of shieldin assembly, elucidates the structural basis of the REV7 conformational dimer, and provides mechanistic insight into orchestration between TLS and NHEJ.

    Organizational Affiliation: 

    Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China. yinyuxin@hsc.pku.edu.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitotic spindle assembly checkpoint protein MAD2B A, B227Homo sapiensMutation(s): 0 
Gene Names: MAD2L2, MAD2B, REV7
Find proteins for Q9UI95 (Homo sapiens)
Explore Q9UI95 
Go to UniProtKB:  Q9UI95
NIH Common Fund Data Resources
PHAROS:  Q9UI95
GTEx:  ENSG00000116670
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Shieldin complex subunit 3 C64Homo sapiensMutation(s): 0 
Gene Names: SHLD3, FLJ26957, RINN1
Find proteins for Q6ZNX1 (Homo sapiens)
Explore Q6ZNX1 
Go to UniProtKB:  Q6ZNX1
NIH Common Fund Data Resources
PHAROS:  Q6ZNX1
GTEx:  ENSG00000253251
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Shieldin complex subunit 2 D54Homo sapiensMutation(s): 0 
Gene Names: SHLD2, FAM35A, RINN2
Find proteins for Q86V20 (Homo sapiens)
Explore Q86V20 
Go to UniProtKB:  Q86V20
NIH Common Fund Data Resources
PHAROS:  Q86V20
GTEx:  ENSG00000122376
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.843α = 90
b = 93.843β = 90
c = 325.377γ = 120
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-28 
  • Released Date: 2020-04-29 
    • Deposition Author(s): Liang, L., Yin, Y.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references