[English] 日本語
Yorodumi
- EMDB-6495: Electron microscopy of apo human XPC complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6495
TitleElectron microscopy of apo human XPC complex
Map dataEMAN2 reconstruction of apo human XPC complex
Sample
  • Sample: Apo human XPC complex
  • 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 / cellular response to interleukin-7 / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / UV-damage excision repair / regulation of mitotic cell cycle phase transition / proteasome binding / centriole replication / site of DNA damage / polyubiquitin modification-dependent protein binding / glial cell projection / embryonic organ development / mRNA transport / 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 / centriole / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / proteasome complex / AURKA Activation by TPX2 / Josephin domain DUBs / ubiquitin binding / regulation of cytokinesis / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / nucleotide-excision repair / DNA Damage Recognition in GG-NER / microtubule cytoskeleton organization / G-protein beta/gamma-subunit complex binding / Formation of Incision Complex in GG-NER / apical part of cell / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / single-stranded DNA binding / protein transport / spermatogenesis / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / ciliary basal body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / cell division / DNA repair / intracellular membrane-bounded organelle / calcium ion binding / centrosome / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Rad4 beta-hairpin domain 2 / 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 2 / 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 / RAD23A/RAD23B, UBA1 domain / 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 / Papain-like cysteine peptidase superfamily / EF-hand domain pair / 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: 25.0 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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6495.tif

Downloads & links

-
Map

FileDownload / File: emd_6495.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMAN2 reconstruction of apo 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: 5.35 / Movie #1: 5.35
Minimum - Maximum-4.96249771 - 16.45165634
Average (Standard dev.)0.0 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-21-21-21
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/NS-21-21-21
NC/NR/NS128128128
D min/max/mean-4.96216.4520.000

-
Supplemental data

-
Sample components

-
Entire : Apo human XPC complex

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

-
Supramolecule #1000: Apo human XPC complex

SupramoleculeName: Apo human XPC complex / 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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.01 mg/mL
BufferpH: 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
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

-
Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Astigmatism was corrected at 80,000 times and 280,000 times magnification.
DateAug 13, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 426 / Average electron dose: 20 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: 2.25 µm / Nominal defocus min: -0.07 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsParticles were selected by DoGPicker in the Appion pipeline.
CTF correctionDetails: whole micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 22777
Final two d classificationNumber classes: 141

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more