2024-11-20 REL RCSB RCSB RCSB 2020-01-02 2020-01-15 2020-01-15 2024-11-20 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM130393 United States Worden EJ Wolberger C Methylation, histone, transcription, ubiquitin, gene regulation, TRANSFERASE-STRUCTURAL PROTEIN-DNA complex Worden EJ Zhang X Wolberger C Elife US 9 2020 31922488 doi:10.7554/eLife.53199 2050-084X 6ven FULLOVERLAP Complex between yeast COMPASS and a ubiquitinated Nucleosome Complex between yeast COMPASS and a ubiquitinated Nucleosome 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Yeast COMPASS 1 8 9 10 11 12 13 Saccharomyces cerevisiae Ubiquitinated Nucleosome 1 1 2 3 4 5 6 7 Xenopus laevis Histone H3.2 Xenopus laevis 0.01525183 2 Escherichia coli LEVO ART(NLE)QTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQ DFKTDLRFQSSAV(NLE)ALQEASEAYLVALFEDTNLCAIHAKRVTI(NLE)PKDIQLARRIRGERA P84233 Histone H4 Xenopus laevis 0.011263230999999999 2 Escherichia coli BL21(DE3) LEVO SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKT VTAMDVVYALKRQGRTLYGFGG P62799 Histone H2A type 1 Xenopus laevis 0.013978240999999999 2 Escherichia coli LEVO SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIP RHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK P06897 Histone H2B 1.1 Xenopus laevis 0.013498715 2 Escherichia coli BL21(DE3) LEVO AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHY NKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTCYTSAK P02281 601 DNA (146-MER) synthetic construct 0.044825559 1 (DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DC)(DG)(DA)(DT) DNA 601 DNA (146-MER) synthetic construct 0.045305851999999994 1 (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA) DNA Ubiquitin Homo sapiens 0.009036393 1 Escherichia coli LEVO GSHMMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC P0CG48 COMPASS component SWD3 Saccharomyces cerevisiae 0.034786637 1 Trichoplusia ni LEVO MFQFVTPVGTQNGLKATCAKISPDGQFLAITQGLNILIYDINRRTVSQTLVTSHARPFSELCWSPDGQCIATASDDFSVE IIHLSYGLLHTFIGHTAPVISLTFNRKGNLLFTSSMDESIKIWDTLNGSLMKTISAHSEAVVSVDVPMNDSSILSSGSYD GLIRIFDAETGHCLKTLTYDKDWKRENGVVPISQVKFSENARYLLVKSLDGVVKIWDCIGGCVVRTFQVQPLEKGVLHHS CGMDFLNPEDGSTPLVISGYENGDIYCWNSDTKSLLQLLDGSLYHHSSPVMSIHCFGNIMCSLALNGDCCLWRWV P38123 COMPASS component SWD1 Saccharomyces cerevisiae 0.048702574 1 Trichoplusia ni LEVO MNILLQDPFAVLKEHPEKLTHTIENPLRTECLQFSPCGDYLALGCANGALVIYDMDTFRPICVPGNMLGAHVRPITSIAW SPDGRLLLTSSRDWSIKLWDLSKPSKPLKEIRFDSPIWGCQWLDAKRRLCVATIFEESDAYVIDFSNDPVASLLSKSDEK QLSSTPDHGYVLVCTVHTKHPNIIIVGTSKGWLDFYKFHSLYQTECIHSLKITSSNIKHLIVSQNGERLAINCSDRTIRQ YEISIDDENSAVELTLEHKYQDVINKLQWNCILFSNNTAEYLVASTHGSSAHELYIWETTSGTLVRVLEGAEEELIDINW DFYSMSIVSNGFESGNVYVWSVVIPPKWSALAPDFEEVEENVDYLEKEDEFDEVDEAEQQQGLEQEEEIAIDLRTREQYD VRGNNLLVERFTIPTDYTRIIKMQSS P39706 Histone-lysine N-methyltransferase, H3 lysine-4 specific Saccharomyces cerevisiae 0.041508487999999996 1 Trichoplusia ni LEVO MHHHHHHGSSDYKDHDGDYKDHDIDYKDDDDKENLYFQGMDLQNAIKDEEDMLILKQLLSTYTPTVTPETSAALEYKIWQ SRRKVLEEEKASDWQIELNGTLFDSELQPGSSFKAEGFRKIADKLKINYLPHRRRVHQPLNTVNIHNERNEYTPELCQRE ESSNKEPSDSVPQEVSSSRDNRASNRRFQQDIEAQKAAIGTESELLSLNQLNKRKKPVMFARSAIHNWGLYALDSIAAKE MIIEYVGERIRQPVAEMREKRYLKNGIGSSYLFRVDENTVIDATKKGGIARFINHCCDPNCTAKIIKVGGRRRIVIYALR DIAASEELTYDYKFEREKDDEERLPCLCGAPNCKGFLN P38827 2.1.1.354 COMPASS component BRE2 Saccharomyces cerevisiae 0.058425301 1 Trichoplusia ni LEVO MKLGIIPYQEGTDIVYKNALQGQQEGKRPNLPQMEATHQIKSSVQGTSYEFVRTEDIPLNRRHFVYRPCSANPFFTILGY GCTEYPFDHSGMSVMDRSEGLSISRDGNDLVSVPDQYGWRTARSDVCIKEGMTYWEVEVIRGGNKKFADGVNNKENADDS VDEVQSGIYEKMHKQVNDTPHLRFGVCRREASLEAPVGFDVYGYGIRDISLESIHEGKLNCVLENGSPLKEGDKIGFLLS LPSIHTQIKQAKEFTKRRIFALNSHMDTMNEPWREDAENGPSRKKLKQETTNKEFQRALLEDIEYNDVVRDQIAIRYKNQ LFFEATDYVKTTKPEYYSSDKRERQDYYQLEDSYLAIFQNGKYLGKAFENLKPLLPPFSELQYNEKFYLGYWQHGEARDE SNDKNTTSAKKKKQQQKKKKGLILRNKYVNNNKLGYYPTISCFNGGTARIISEEDKLEYLDQIRSAYCVDGNSKVNTLDT LYKEQIAEDIVWDIIDELEQIALQQ P43132 COMPASS component SDC1 Saccharomyces cerevisiae 0.019466219 2 Trichoplusia ni LEVO MNESENSPQHNEVTVPMVEDTSSNADIPMEQIQREDNKNYDKHDNECFDMNGNHNNNSDNLQFDSVPSSATKDLKNIKSV TNQNVKIEESSSTNSVIEESSEPKISKLENVNLAATVGGSQTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQ SNILKSGEKESNASK Q03323 COMPASS component SPP1 Saccharomyces cerevisiae 0.045489457 1 Trichoplusia ni LEVO MWSHPQFEKGGGSGGGSGGSSAWSHPQFEKGSENLYFQGSLPQWCPPHSTLKRNPTTGEDVYCICKRPDYGELMVGCDGC DDWFHFTCLHIPEQFKDLVFSFYCPYCQAGITGKNKDAIINGEGSLPKTLWKRKCRISDCYKPCLQDSKYCSEEHGREFV NDIWSRLKTDEDRAVVKKMVEQTGHIDKFKKFGQLDFIDNNIVVKTDDEKEIFDQIVVRDMTLKTLEDDLQEVQEISLPL FKKKLELLEVYLGWLDNVYTEMRKLDDDAASHVECGKEDSKGTKRKKKKNSSRSRARKNICGYCSTYERIPCSVEEFVRD FGSNEEATKIHEVCTKWKCNRHLDWVSTNQEQYLQQIDSLESMQERLQHLIQARKKQLNIQYYEEILRRGL Q03012 ZINC ION 6.5409e-05 1 ZN S-ADENOSYLMETHIONINE 0.000398437 1 SAM singleParticle particle 0.5 7.5 30.0 Tris 100.0 NaCl Sodium Chloride 2.0 DTT 25.0 S-adenosyl methionine Quantifoil R2/2 COPPER 200 CARBON HOLEY ARRAY GLOW DISCHARGE 45 AIR

15 mA

ETHANE 100 277 FEI VITROBOT MARK III

blot force 5 3.5 sec blot time.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 -1.0 2.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 1 5784 2.96 50.0 1 2036654

Relion template-based picking from 3D model

6BX3

Also used 1KX3

C1 3.37 FSC 0.143 CUT-OFF RELION 3 650847 RANDOM ASSIGNMENT RELION 3 MAXIMUM LIKELIHOOD RELION 3 4 RELION 3 6CHG PDB experimental model 6BX3 F PDB experimental model 6BX3 E 799-850 PDB experimental model 6NJ9 PDB experimental model OTHER REAL 110.0 emd_21157_msk_1.map emd_21157_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.013671658 0.04931196 -0.000006451728 0.0013385295 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-21157:::: Final, unsharpened map emd_21157_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.014160246 0.051761013 -0.000003256153 0.0014567632 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-21157:::: emd_21157_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.015934337 0.052449025 -0.0000044657904 0.0014563287 1.08 1.08 1.08 AUTHOR ::::EMDATABANK.org::::EMD-21157::::