Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Architecture of the human XPC DNA repair and stem cell coactivator complex. Authors: Elisa T Zhang / Yuan He / Patricia Grob / Yick W Fong / Eva Nogales / Robert Tjian / Abstract: The Xeroderma pigmentosum complementation group C (XPC) complex is a versatile factor involved in both nucleotide excision repair and transcriptional coactivation as a critical component of the ...The Xeroderma pigmentosum complementation group C (XPC) complex is a versatile factor involved in both nucleotide excision repair and transcriptional coactivation as a critical component of the NANOG, OCT4, and SOX2 pluripotency gene regulatory network. Here we present the structure of the human holo-XPC complex determined by single-particle electron microscopy to reveal a flexible, ear-shaped structure that undergoes localized loss of order upon DNA binding. We also determined the structure of the complete yeast homolog Rad4 holo-complex to find a similar overall architecture to the human complex, consistent with their shared DNA repair functions. Localized differences between these structures reflect an intriguing phylogenetic divergence in transcriptional capabilities that we present here. Having positioned the constituent subunits by tagging and deletion, we propose a model of key interaction interfaces that reveals the structural basis for this difference in functional conservation. Together, our findings establish a framework for understanding the structure-function relationships of the XPC complex in the interplay between transcription and DNA repair.
History
Deposition
Nov 1, 2015
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Header (metadata) release
Nov 18, 2015
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Map release
Nov 18, 2015
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Update
Dec 16, 2015
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Current status
Dec 16, 2015
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
UniProtKB: DNA repair protein RAD33 / InterPro: Rad33
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Experimental details
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Structure determination
Method
negative staining
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.01 mg/mL
Buffer
pH: 7.6 Details: 300 mM KCl, 50 mM HEPES, 0.1% NP-40 alternative, 10% glycerol, 0.1 mM EDTA, 1 mM MgCl2, 1 mM TCEP, 1 mM DTT
Staining
Type: NEGATIVE Details: Grids with adsorbed protein were floated on 2 successive droplets of buffer G (300 mM KCl, 25 mM HEPES ph 7.6, 3% w/v trehalose, 0.01% NP-40 alternative, 1 mM TCEP, 1 mM DTT, 0.1 mM EDTA, 1 ...Details: Grids with adsorbed protein were floated on 2 successive droplets of buffer G (300 mM KCl, 25 mM HEPES ph 7.6, 3% w/v trehalose, 0.01% NP-40 alternative, 1 mM TCEP, 1 mM DTT, 0.1 mM EDTA, 1 mM MgCl2) and subsequently floated on 4 successive 1% w/v uranyl droplets for 10 seconds each.
Grid
Details: 400 mesh copper grid with thin carbon support
Vitrification
Cryogen name: NONE / Instrument: OTHER
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Electron microscopy
Microscope
FEI TECNAI F20
Alignment procedure
Legacy - Astigmatism: Astigmatism was corrected at 80,000 times and 280,000 times magnification.
Date
Aug 10, 2014
Image recording
Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 486 / Average electron dose: 30 e/Å2 / Bits/pixel: 32
Tilt angle min
0
Tilt angle max
0
Electron beam
Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
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