2019-11-06 REL PDBe PDBe PDBe 2016-11-25 2016-12-28 2017-04-05 2019-11-06 Wellcome Trust United Kingdom 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 other EM volume
EM map of Chd1-1305delta57-88 bound to 601-Nucleosome
 EMD-3517 associated EM volume Chd1-Nucleosome complex Chd1-Nucleosome complex 0 1
S.Cerevisiae chromatin remodelling enzyme in complex with 601-nucleosome
0.4 Chd1 1 Saccharomyces cerevisiae Escherichia coli Nucleosome 1 Xenopus laevis Escherichia coli Chromodomain Helicase DNA binding protein
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 100 277 FEI VITROBOT MARK IV
Grids are double side blotted with 2sec blotting time and blotting force 10.
This sample was monodisperse. One Chd1 molecule bound to one Nucleosome.
 FEI TECNAI 20 SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.0 1.5 1.5 5.0 5.0 68000. 68000. GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER NITROGEN 70.0 70.0
Preliminary grid screen was done manually and then data collection was performed automatically using EMTools-EMMenu
TVIPS TEMCAM-F416 (4k x 4k) 4096 4096 15.6 1 140 2.0 22.0 1
Images were manually inspected for any contamination or damage.
47000
Initial template for autopicking is made from manually picked particles. Then RELION-1.3 autopick routine was used for autopicking
 CTFFIND 3 1KX5
Nucleosome structure 1KX5 was converted into map of pixel size 1.58, low pass filtered and used as initial model.
 2 C1 FOURIER SPACE 20.0 FSC 0.143 CUT-OFF RELION 1.3 36324 ANGULAR RECONSTITUTION RELION 1.3 PROJECTION MATCHING CC 7.5 RELION 1.3 2 17000.0 RELION 1.3 emd_3517.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 316.0 316.0 316.0 90.0 90.0 90.0 X Y Z -0.021911494 0.14400715 0.0008408567 0.0077083986 1.58 1.58 1.58 0.0145 AUTHOR S.Cerevisiae Chd1 bound to 601-Nucleosome 1KX5 A B C D E F G H I J 3MWY A 175-932 2XB0 X 1010-1274 RIGID BODY FIT Cross-correlation coefficient REAL 2800.0