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- EMDB-12817: Chaetomium thermophilum Chl1 Helicase -

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Basic information

Entry
Database: EMDB / ID: EMD-12817
TitleChaetomium thermophilum Chl1 Helicase
Map dataFinal map after SideSplitter refinement.
Sample
  • Complex: Chl1 helicase
    • Protein or peptide: Chl1
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / DNA 5'-3' helicase / nucleobase-containing compound metabolic process / DNA helicase activity / DNA binding / ATP binding / nucleus
Similarity search - Function
ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain ...ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent DNA helicase CHL1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsHodakova Z / Singleton MR
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)FC001155 United Kingdom
Wellcome TrustFC001155 United Kingdom
Cancer Research UKFC001155 United Kingdom
CitationJournal: PLoS One / Year: 2021
Title: Structural characterisation of the Chaetomium thermophilum Chl1 helicase.
Authors: Zuzana Hodáková / Andrea Nans / Simone Kunzelmann / Shahid Mehmood / Ian Taylor / Frank Uhlmann / Peter Cherepanov / Martin R Singleton /
Abstract: Chl1 is a member of the XPD family of 5'-3' DNA helicases, which perform a variety of roles in genome maintenance and transmission. They possess a variety of unique structural features, including the ...Chl1 is a member of the XPD family of 5'-3' DNA helicases, which perform a variety of roles in genome maintenance and transmission. They possess a variety of unique structural features, including the presence of a highly variable, partially-ordered insertion in the helicase domain 1. Chl1 has been shown to be required for chromosome segregation in yeast due to its role in the formation of persistent chromosome cohesion during S-phase. Here we present structural and biochemical data to show that Chl1 has the same overall domain organisation as other members of the XPD family, but with some conformational alterations. We also present data suggesting the insert domain in Chl1 regulates its DNA binding.
History
DepositionApr 28, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12817.png

Downloads & links

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Map

FileDownload / File: emd_12817.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map after SideSplitter refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 120 pix.
= 201.36 Å		1.68 Å/pix.
x 120 pix.
= 201.36 Å		1.68 Å/pix.
x 120 pix.
= 201.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.678 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.086543344 - 0.13410006
Average (Standard dev.)0.00041872868 (±0.0057615903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 201.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6781.6781.678
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z201.360201.360201.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.0870.1340.000

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Supplemental data

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Sample components

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Entire : Chl1 helicase

EntireName: Chl1 helicase
Components
  • Complex: Chl1 helicase
    • Protein or peptide: Chl1

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Supramolecule #1: Chl1 helicase

SupramoleculeName: Chl1 helicase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Chl1

MacromoleculeName: Chl1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQSGTDI KSDEGLEAPN NNEHINFHHP YTPYDVQLQF MRTVYNILEK GGGQVGILES PTGTGKSLSL ICSALTWLRH HKRSRFSASF DETSAAMAGE PDWMIEAALR RKRQELARLW EEREAALRKA REKERQEEEK ...String:
MWSHPQFEKG GGSGGGSGGG SWSHPQFEKE NLYFQSGTDI KSDEGLEAPN NNEHINFHHP YTPYDVQLQF MRTVYNILEK GGGQVGILES PTGTGKSLSL ICSALTWLRH HKRSRFSASF DETSAAMAGE PDWMIEAALR RKRQELARLW EEREAALRKA REKERQEEEK AAMGLHGRSV KRARVDDGEY GKRKKGEIDE EREFLVGDWA DGTVTGDGLA GLSKETRELM AKVGLGGAQG KEGEEDCSLI EEEVKIYYTS RTHSQIAQFI GELRRPAFPT SIPEDMLSTD NLGKGPPTEP VKQVPLSSRQ KLCINPSVAR LNSLSAINDR CTELQQGKSG HKCPFIPNAD NLKQVHEFRD TVLASLPDIE DLYRVGKDLQ VCPYYASREA IPGAEVVTLP YPLLLQKSAR EALGIKLEGN IVIIDEAHNI MDAIANVHAA EIRLSELRRA REMLGVYVKR FGKKLKGENR MMVAQVGRVV ESLSEWLNTA LNGKGDHGIV DSNSLLKARG ADQINLYQLI KYIQDSKLAY KVESYVSHKE EEEAQGQGKT STTTPVLHTL VSFLSALTNL STEGRIFYEK LLTTPSDIKL SYLLLSPTHA FSSIVSAARA VILAGGTMSP FDDYKAHLFP MLSEDKITTL SCGHVIPSSN LFVWTLASTR PGQQGSAAAS DAFEFSFQKR SDPAMIRQLG LVLLNICSVV PDGVVVFFPS YSYLDEVVAA WQAPETQNGP SVSFQRKQTL WDRLAAKKTL FRESKGGSSD EILQQYSDAI FSAGTASRQQ LDPTGRGGAL LLSVVGGKLS EGINFSDRLG RCVVVVGLPY PNINSPEWKA RIEYVETAAI ARLTSSKTSR FEGEGDKTQS RALTREEALP LARQVARDFY ENACMRAVNQ SIGRAIRHRG DYAAVVLIDR RFGTDRIRGK LPGWIRQGMV EGSENKGLAG LMSGLGSFFR GRSG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8.5
GridModel: C-flat-1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 74.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88452
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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