2017-08-02 REL PDBe PDBe PDBe 2016-11-15 2016-12-14 2017-04-05 2017-08-02 Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes Sundaramoorthy R Owen-Hughes T Sundaramoorthy R Hughes AL Singh V Wiechens N Ryan DP El-Mkami H Petoukhov M Svergun DI Treutlein B Quack S Fischer M Michaelis J Bottcher B Norman DG Owen-Hughes T Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. Elife US 6 2017 28332978 doi:10.7554/eLife.22510 2050-084X EMD-3502 associated EM volume Chd1-Nucleosome complex Chd1-Nucleosome complex 0 1
S.cerevisiae chromatin remodelling enzyme in complex with Nucleosome
0.4 chd1 1 Saccharomyces cerevisiae Escherichia coli nucleosome 1 Xenopus laevis Escherichia coli Chromodomain-Helicase-DNA containing protein MAAKDISTEVLQNPELYGLRRSHRAAAHQQNYFNDSDDEDDEDNIKQSRRKRMTTIEDDE DEFEDEEGEEDSGEDEDEEDFEEDDDYYGSPIKQNRSKPKSRTKSKSKSKPKSQSEKQST VKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGID IVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLK RLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLED GTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPR FEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIF ARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGK KTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLI TGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKK DVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASN HPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQM VRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINL MTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILE YAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAED HVTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQ LEMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYK AILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEK HATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDL KYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRD DPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYL LSFLRGGLNTKSPSADIGSKKLPTGPSKKRQRKPANHSKSMTPEI other singleParticle particle 0.2 7.5 20.0 Tris tris(hydroxymethyl)aminomethane 50.0 NaCl Sodium Chloride
Solutions were made fresh
 Quantifoil COPPER/RHODIUM 400 GLOW DISCHARGE AIR 101.325 ETHANE 100.00 277 FEI VITROBOT MARK IV
This sample was monodisperse. One Chd1 enzyme bound to the Nucleosome
FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.8 1.8 4.0 4.0 59000. 59000. FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON II (4k x 4k) INTEGRATING 4096 4096 14.0 4-18 1 2560 1.0 2.27
Images are collected in movie mode at 22 images per second
 1
The selected images were high pass filtered and framwise movie corrected for drift.
280000
Particles are picked using RELION 1.4 autopick routine
 CTFFIND 4 1KX5
Nucleosome structure 1KX5 was converted into map of pixel size 1.34, low pass filtered and used as a initial model
 2 C1 FOURIER SPACE 15.0 FSC 0.143 CUT-OFF RELION 1.4
RELION 1.4 was used for the reconstruction.
52208 ANGULAR RECONSTITUTION PROJECTION MATCHING CC 3.5 RELION 1.4 2 26000. emd_3502.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 335.0 335.0 335.0 90.0 90.0 90.0 X Y Z -0.054358844 0.20822248 0.0010571269 0.012176228 1.34 1.34 1.34 0.049 AUTHOR Structure of S.cerevisiae chromatin remodeling enzyme Chd1 bound to Nucleosome. 1KX5 A B C D E F G H I J 3MWY A 175-932 3TED A B C 1010-1274 RIGID BODY FIT Cross-correlation coefficient REAL emd_3502_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 335.0 335.0 335.0 90.0 90.0 90.0 X Y Z -0.027375946 0.097225904 0.00052098767 0.0058889086 1.34 1.34 1.34 0.05 AUTHOR Half map1 of the reconstruction emd_3502_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 250 250 250 0 0 0 250 250 250 335.0 335.0 335.0 90.0 90.0 90.0 X Y Z -0.025301374 0.09491147 0.00053613924 0.005880291 1.34 1.34 1.34 0.05 AUTHOR Half map2 of the reconstruction