5ICA

Structure of the CTD complex of UTP12, Utp13, Utp1 and Utp21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

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This is version 1.1 of the entry. See complete history


Literature

Integrative structural analysis of the UTPB complex, an early assembly factor for eukaryotic small ribosomal subunits

Zhang, C.Sun, Q.Chen, R.Chen, X.Lin, J.Ye, K.

(2016) Nucleic Acids Res 44: 7475-7486

  • DOI: 10.1093/nar/gkw562
  • Primary Citation of Related Structures:  
    5IC7, 5IC8, 5IC9, 5ICA

  • PubMed Abstract: 
  • Ribosome assembly is an essential and conserved cellular process in eukaryotes that requires numerous assembly factors. The six-subunit UTPB complex is an essential component of the 90S precursor of the small ribosomal subunit. Here, we analyzed the molecular architecture of UTPB using an integrative structural biology approach ...

    Ribosome assembly is an essential and conserved cellular process in eukaryotes that requires numerous assembly factors. The six-subunit UTPB complex is an essential component of the 90S precursor of the small ribosomal subunit. Here, we analyzed the molecular architecture of UTPB using an integrative structural biology approach. We mapped the major interactions that associate each of six UTPB proteins. Crystallographic studies showed that Utp1, Utp21, Utp12 and Utp13 are evolutionarily related and form a dimer of dimers (Utp1-Utp21, Utp12-Utp13) through their homologous helical C-terminal domains. Molecular docking with crosslinking restraints showed that the WD domains of Utp12 and Utp13 are associated, as are the WD domains of Utp1, Utp21 and Utp18. Electron microscopy images of the entire UTPB complex revealed that it predominantly adopts elongated conformations and possesses internal flexibility. We also determined crystal structures of the WD domain of Utp18 and the HAT and deviant HAT domains of Utp6. A structural model of UTPB was derived based on these data.


    Organizational Affiliation

    Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China Beijing Key Laboratory of Noncoding RNA, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China yekeqiong@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinA163Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0003430
UniProt
Find proteins for G0RZL9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0RZL9
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UniProt GroupG0RZL9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinB152Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0065530
UniProt
Find proteins for G0SG95 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SG95
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Putative U3 snoRNP proteinC244Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0037800
UniProt
Find proteins for G0S872 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0S872
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Periodic tryptophan protein 2-like proteinD149Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0061240
UniProt
Find proteins for G0SF93 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SF93 
Go to UniProtKB:  G0SF93
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UniProt GroupG0SF93
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.695α = 90
b = 121.695β = 90
c = 167.49γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references