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- EMDB-3517: Structural reorganization of the chromatin remodeling enzyme Chd1... -

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Basic information

Entry
Database: EMDB / ID: 3517
TitleStructural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
Map dataS.Cerevisiae Chd1 bound to 601-Nucleosome
SampleChd1-Nucleosome complex:
Chd1 / Nucleosome / nucleic-acidNucleic acid
SourceSaccharomyces cerevisiae (baker's yeast) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / 20 Å resolution
AuthorsSundaramoorthy R / Owen-Hughes T
CitationJournal: Elife / Year: 2017
Title: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
Authors: Ramasubramanian Sundaramoorthy / Amanda L Hughes / Vijender Singh / Nicola Wiechens / Daniel P Ryan / Hassane El-Mkami / Maxim Petoukhov / Dmitri I Svergun / Barbara Treutlein / Salina Quack / Monika Fischer / Jens Michaelis / Bettina Böttcher / David G Norman / Tom Owen-Hughes
DateDeposition: Nov 25, 2016 / Header (metadata) release: Dec 28, 2016 / Map release: Apr 5, 2017 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3517.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.58 Å/pix.
= 316. Å
200 pix
1.58 Å/pix.
= 316. Å
200 pix
1.58 Å/pix.
= 316. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density
Contour Level:0.0145 (by author), 0.0145 (movie #1):
Minimum - Maximum-0.021911494 - 0.14400715
Average (Standard dev.)0.0008408567 (0.0077083986)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 316.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z316.000316.000316.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0220.1440.001

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Supplemental data

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Sample components

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Entire Chd1-Nucleosome complex

EntireName: Chd1-Nucleosome complex
Details: S.Cerevisiae chromatin remodelling enzyme in complex with 601-nucleosome
Number of components: 4

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Component #1: protein, Chd1-Nucleosome complex

ProteinName: Chd1-Nucleosome complex
Details: S.Cerevisiae chromatin remodelling enzyme in complex with 601-nucleosome
Recombinant expression: No
MassTheoretical: 400 kDa

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Component #2: protein, Chd1

ProteinName: Chd1 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Nucleosome

ProteinName: Nucleosome / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: nucleic-acid, Chromodomain Helicase DNA binding protein

Nucleic-acidName: Chromodomain Helicase DNA binding protein / Class: OTHER / Details: Protein / Structure: OTHER / Synthetic: No
Sequence:
MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE DEFEDEEGEE DSGEDEDEED FEEDDDYYGS PIKQNRSKPK SRTKSKSKSK PKSQSEKQST VKIPTRFSNR QNKTVNYNID YSDDDLLESE DDYGSEEALS EENVHEASAN PQPEDFHGID IVINHRLKTS LEEGKVLEKT VPDLNNCKEN YEFLIKWTDE SHLHNTWETY ESIGQVRGLK RLDNYCKQFI IEDQQVRLDP YVTAEDIEIM DMERERRLDE FEEFHVPERI IDSQRASLED GTSQLQYLVK WRRLNYDEAT WENATDIVKL APEQVKHFQN RENSKILPQY SSNYTSQRPR FEKLSVQPPF IKGGELRDFQ LTGINWMAFL WSKGDNGILA DEMGLGKTVQ TVAFISWLIF ARRQNGPHII VVPLSTMPAW LDTFEKWAPD LNCICYMGNQ KSRDTIREYE FYTNPRAKGK KTMKFNVLLT TYEYILKDRA ELGSIKWQFM AVDEAHRLKN AESSLYESLN SFKVANRMLI TGTPLQNNIK ELAALVNFLM PGRFTIDQEI DFENQDEEQE EYIHDLHRRI QPFILRRLKK DVEKSLPSKT ERILRVELSD VQTEYYKNIL TKNYSALTAG AKGGHFSLLN IMNELKKASN HPYLFDNAEE RVLQKFGDGK MTRENVLRGL IMSSGKMVLL DQLLTRLKKD GHRVLIFSQM VRMLDILGDY LSIKGINFQR LDGTVPSAQR RISIDHFNSP DSNDFVFLLS TRAGGLGINL MTADTVVIFD SDWNPQADLQ AMARAHRIGQ KNHVMVYRLV SKDTVEEEVL ERARKKMILE YAIISLGVTD GNKYTKKNEP NAGELSAILK FGAGNMFTAT DNQKKLEDLN LDDVLNHAED HVTTPDLGES HLGGEEFLKQ FEVTDYKADI DWDDIIPEEE LKKLQDEEQK RKDEEYVKEQ LEMMNRRDNA LKKIKNSVNG DGTAANSDSD DDSTSRSSRR RARANDMDSI GESEVRALYK AILKFGNLKE ILDELIADGT LPVKSFEKYG ETYDEMMEAA KDCVHEEEKN RKEILEKLEK HATAYRAKLK SGEIKAENQP KDNPLTRLSL KKREKKAVLF NFKGVKSLNA ESLLSRVEDL KYLKNLINSN YKDDPLKFSL GNNTPKPVQN WSSNWTKEED EKLLIGVFKY GYGSWTQIRD DPFLGITDKI FLNEVHNPVA KKSASSSDTT PTPSKKGKGI TGSSKKVPGA IHLGRRVDYL LSFLRGGLNT KSPSADIGSK KLPTGPSKKR QRKPANHSKS MTPEI

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / Buffer solution: Solutions were made fresh. / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Grids are double side blotted with 2sec blotting time and blotting force 10.

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Details: Preliminary grid screen was done manually and then data collection was performed automatically using EMTools-EMMenu
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 22 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 68000.0 X (nominal), 68000.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 5000.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 70.0 - 70.0 K)
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 140 / Sampling size: 15.6 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 36324
Details: Images were manually inspected for any contamination or damage.
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Cross-correlation coefficient / Refinement space: REAL
Input PDB model: 1KX5, 3MWY, 2XB0
Chain ID: A, B, C, D, E, F, G, H, I, J, A, X

Overall bvalue: 28

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