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- EMDB-6498: Electron microscopy of DNA-bound human XPC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6498
TitleElectron microscopy of DNA-bound human XPC complex
Map dataReconstruction of dsDNA-bound human XPC complex
Sample
  • Sample: DNA-bound human XPC complex by RELION
  • Protein or peptide: Xeroderma pigmentosum group C-complementing protein
  • Protein or peptide: RAD23 homolog B
  • Protein or peptide: Centrin-2
Keywordstranscription / DNA repair / stem cells
Function / homology
Function and homology information


heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / 9+2 motile cilium / photoreceptor connecting cilium / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription export complex 2 ...heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / nucleotide-excision repair complex / 9+2 motile cilium / photoreceptor connecting cilium / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription export complex 2 / heterotrimeric G-protein binding / response to auditory stimulus / nuclear pore nuclear basket / bubble DNA binding / UV-damage excision repair / cellular response to interleukin-7 / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / regulation of mitotic cell cycle phase transition / proteasome binding / site of DNA damage / centriole replication / polyubiquitin modification-dependent protein binding / mRNA transport / embryonic organ development / mismatch repair / SUMOylation of DNA damage response and repair proteins / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / proteasome complex / Josephin domain DUBs / ciliary basal body / regulation of cytokinesis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / nucleotide-excision repair / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding / Formation of Incision Complex in GG-NER / Regulation of PLK1 Activity at G2/M Transition / protein transport / apical part of cell / mitotic cell cycle / single-stranded DNA binding / microtubule binding / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / intracellular membrane-bounded organelle / DNA repair / centrosome / calcium ion binding / protein-containing complex binding / chromatin / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Rad4 beta-hairpin domain 2 / RAD23A/RAD23B, UBA1 domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily ...: / Rad4 beta-hairpin domain 2 / RAD23A/RAD23B, UBA1 domain / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Transglutaminase-like superfamily / UBA/TS-N domain / Ubiquitin associated domain / ATP-dependent RNA helicase DEAD-box, conserved site / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / : / EF-hand domain pair / Papain-like cysteine peptidase superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Centrin-2 / UV excision repair protein RAD23 homolog B / DNA repair protein complementing XP-C cells
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsZhang ET / He Y / Grob P / Fong YW / Nogales E / Tjian R
CitationJournal: 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
DepositionNov 1, 2015-
Header (metadata) releaseNov 18, 2015-
Map releaseNov 18, 2015-
UpdateDec 16, 2015-
Current statusDec 16, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0817
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0817
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6498.tif

Downloads & links

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Map

FileDownload / File: emd_6498.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of dsDNA-bound human XPC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.01 Å/pix.
x 128 pix.
= 385.28 Å		3.01 Å/pix.
x 128 pix.
= 385.28 Å		3.01 Å/pix.
x 128 pix.
= 385.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0817 / Movie #1: 0.0817
Minimum - Maximum-0.0262924 - 0.21097681
Average (Standard dev.)0.00163173 (±0.01414377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 385.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.013.013.01
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z385.280385.280385.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-189
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0260.2110.002

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Supplemental data

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Sample components

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Entire : DNA-bound human XPC complex by RELION

EntireName: DNA-bound human XPC complex by RELION
Components
  • Sample: DNA-bound human XPC complex by RELION
  • Protein or peptide: Xeroderma pigmentosum group C-complementing protein
  • Protein or peptide: RAD23 homolog B
  • Protein or peptide: Centrin-2

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Supramolecule #1000: DNA-bound human XPC complex by RELION

SupramoleculeName: DNA-bound human XPC complex by RELION / type: sample / ID: 1000
Details: Monodisperse. Thawed from -80 degrees Celsius and placed on ice immediately prior to grid preparation.
Oligomeric state: heterotrimer / Number unique components: 3
Molecular weightExperimental: 200 KDa / Theoretical: 200 KDa / Method: SDS-PAGE, size exclusion chromatography

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Macromolecule #1: Xeroderma pigmentosum group C-complementing protein

MacromoleculeName: Xeroderma pigmentosum group C-complementing protein / type: protein_or_peptide / ID: 1
Name.synonym: XPC, p125, DNA repair protein complementing XP-C cells
Details: contains N-terminal 6xHis and TEV cleavage site / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human / Location in cell: nucleus, cytoplasm
Molecular weightExperimental: 125 KDa / Theoretical: 125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9
SequenceUniProtKB: DNA repair protein complementing XP-C cells / GO: XPC complex

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Macromolecule #2: RAD23 homolog B

MacromoleculeName: RAD23 homolog B / type: protein_or_peptide / ID: 2
Name.synonym: RAD23B, HR23B, HHR23B, p58, XP-C repair-complementing complex 58 kDa protein
Details: contains N-terminal 1xFLAG tag / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human / Location in cell: nucleus, cytoplasm
Molecular weightExperimental: 58 KDa / Theoretical: 58 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9
SequenceUniProtKB: UV excision repair protein RAD23 homolog B / GO: XPC complex / InterPro: UV excision repair protein Rad23

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Macromolecule #3: Centrin-2

MacromoleculeName: Centrin-2 / type: protein_or_peptide / ID: 3 / Name.synonym: CETN2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human / Location in cell: nucleus, cytoplasm, centrosomes
Molecular weightExperimental: 18 KDa / Theoretical: 18 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9
SequenceUniProtKB: Centrin-2 / GO: XPC complex / InterPro: INTERPRO: IPR029528

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
StainingType: 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.
GridDetails: 400 mesh copper grid with thin carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Astigmatism was corrected at 80,000 times and 280,000 times magnification.
DateJun 22, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 980 / Average electron dose: 30 e/Å2 / Bits/pixel: 32
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.44 µm / Nominal defocus min: 0.43 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected by DoGPicker in the Appion pipeline.
CTF correctionDetails: whole micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 69150

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