5JA4

Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex.

Saredi, G., Huang, H., Hammond, C.M., Alabert, C., Bekker-Jensen, S., Forne, I., Reveron-Gomez, N., Foster, B.M., Mlejnkova, L., Bartke, T., Cejka, P., Mailand, N., Imhof, A., Patel, D.J., Groth, A.

(2016) Nature 534: 714-718

  • DOI: 10.1038/nature18312
  • Primary Citation of Related Structures:  
    5JA4

  • PubMed Abstract: 

    • After DNA replication, chromosomal processes including DNA repair and transcription take place in the context of sister chromatids. While cell cycle regulation can guide these processes globally, mechanisms to distinguish pre- and post-replicative states locally remain unknown ...

    After DNA replication, chromosomal processes including DNA repair and transcription take place in the context of sister chromatids. While cell cycle regulation can guide these processes globally, mechanisms to distinguish pre- and post-replicative states locally remain unknown. Here we reveal that new histones incorporated during DNA replication provide a signature of post-replicative chromatin, read by the human TONSL–MMS22L homologous recombination complex. We identify the TONSL ankyrin repeat domain (ARD) as a reader of histone H4 tails unmethylated at K20 (H4K20me0), which are specific to new histones incorporated during DNA replication and mark post-replicative chromatin until the G2/M phase of the cell cycle. Accordingly, TONSL–MMS22L binds new histones H3–H4 both before and after incorporation into nucleosomes, remaining on replicated chromatin until late G2/M. H4K20me0 recognition is required for TONSL–MMS22L binding to chromatin and accumulation at challenged replication forks and DNA lesions. Consequently, TONSL ARD mutants are toxic, compromising genome stability, cell viability and resistance to replication stress. Together, these data reveal a histone-reader-based mechanism for recognizing the post-replicative state, offering a new angle to understand DNA repair with the potential for targeted cancer therapy.

    Organizational Affiliation: 

    Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3A79Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B, H3-3A, H3-3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
PHAROS:  P84243
GTEx:  ENSG00000163041 
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UniProt GroupP84243
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B102Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2C70Homo sapiensMutation(s): 0 
Gene Names: MCM2, BM28, CCNL1, CDCL1, KIAA0030
EC: 3.6.4.12
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Find proteins for P49736 (Homo sapiens)
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Go to UniProtKB:  P49736
PHAROS:  P49736
GTEx:  ENSG00000073111 
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UniProt GroupP49736
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tonsoku-like proteinD181Homo sapiensMutation(s): 0 
Gene Names: TONSL, IKBR, NFKBIL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HA7 (Homo sapiens)
Explore Q96HA7 
Go to UniProtKB:  Q96HA7
PHAROS:  Q96HA7
GTEx:  ENSG00000160949 
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UniProt GroupQ96HA7
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES
Download Ideal Coordinates CCD File 
E [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth B],
G [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.506α = 90
b = 139.506β = 90
c = 72.896γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-04-11 
  • Released Date: 2016-06-15 
    • Deposition Author(s): Huang, H., Patel, D.

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references
  • Version 1.2: 2016-07-13
    Changes: Database references