3QQC

Crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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This is version 1.3 of the entry. See complete history. 


Literature

Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity.

Martinez-Rucobo, F.W., Sainsbury, S., Cheung, A.C., Cramer, P.

(2011) EMBO J 30: 1302-1310

  • DOI: 10.1038/emboj.2011.64
  • Primary Citation of Related Structures:  
    3QQC

  • PubMed Abstract: 

    • Related RNA polymerases (RNAPs) carry out cellular gene transcription in all three kingdoms of life. The universal conservation of the transcription machinery extends to a single RNAP-associated factor, Spt5 (or NusG in bacteria), which renders RNAP processive and may have arisen early to permit evolution of long genes ...

    Related RNA polymerases (RNAPs) carry out cellular gene transcription in all three kingdoms of life. The universal conservation of the transcription machinery extends to a single RNAP-associated factor, Spt5 (or NusG in bacteria), which renders RNAP processive and may have arisen early to permit evolution of long genes. Spt5 associates with Spt4 to form the Spt4/5 heterodimer. Here, we present the crystal structure of archaeal Spt4/5 bound to the RNAP clamp domain, which forms one side of the RNAP active centre cleft. The structure revealed a conserved Spt5-RNAP interface and enabled modelling of complexes of Spt4/5 counterparts with RNAPs from all kingdoms of life, and of the complete yeast RNAP II elongation complex with bound Spt4/5. The N-terminal NGN domain of Spt5/NusG closes the RNAP active centre cleft to lock nucleic acids and render the elongation complex stable and processive. The C-terminal KOW1 domain is mobile, but its location is restricted to a region between the RNAP clamp and wall above the RNA exit tunnel, where it may interact with RNA and/or other factors.

    Organizational Affiliation: 

    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit b, DNA-directed RNA polymerase subunit a', DNA-directed RNA polymerase subunit A''A436Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1563
EC: 2.7.7.6
UniProt
Find proteins for Q8U0M4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U0M4 
Go to UniProtKB:  Q8U0M4
Find proteins for Q8U0M3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Go to UniProtKB:  Q8U0M3
Find proteins for Q8U0M5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U0M5 
Go to UniProtKB:  Q8U0M5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8U0M5Q8U0M3Q8U0M4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription antitermination protein nusGB [auth D]163Pyrococcus furiosusMutation(s): 0 
Gene Names: PF1990
UniProt
Find proteins for Q8TZK1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZK1 
Go to UniProtKB:  Q8TZK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TZK1
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase, subunit e''C [auth E]61Pyrococcus furiosusMutation(s): 0 
Gene Names: PF0255
UniProt
Find proteins for Q8U440 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U440 
Go to UniProtKB:  Q8U440
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U440
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.57α = 90
b = 107.04β = 97.1
c = 51.09γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-09-18
    Changes: Derived calculations
  • Version 1.3: 2017-08-09
    Changes: Data collection, Refinement description, Source and taxonomy