2024-05-15 REL PDBe PDBe PDBe 2018-07-18 2019-07-03 2019-07-10 2024-05-15 Schenk AD Julius R Cavadini S Thoma NH Deubiquitinase complex, DUB, Lysine-63 linkage specific, BRCC36-containing, BRCA1A binding, SIGNALING PROTEIN Rabl J Bunker RD Schenk AD Cavadini S Gill ME Abdulrahman W Andres-Pons A Luijsterburg MS Ibrahim AFM Branigan E Aguirre JD Marceau AH Guerillon C Bouwmeester T Hassiepen U Peters AHFM Renatus M Gelman L Rubin SM Mailand N van Attikum H Hay RT Thoma NH Mol.Cell US 75 483 497.e9 2019 31253574 doi:10.1016/j.molcel.2019.06.002 1097-2765 2168 MOCEFL 6h3c FULLOVERLAP BRISC complex bound to SHMT2 alpha BRISC complex bound to SHMT2 alpha 0 1 2 3 4 5 0.438 BRISC complex 1 1 2 3 4 Homo sapiens SHMT2 alpha 1 5 Homo sapiens BRISC complex subunit Abraxas 2 Homo sapiens 0.049256246 2 Trichoplusia ni LEVO MHHHHHHVDENLYFQGGGRMAASISGYTFSAVCFHSANSNADHEGFLLGEVRQEETFSISDSQISNTEFLQVIEIHNHQP CSKLFSFYDYASKVNEESLDRILKDRRKKVIGWYRFRRNTQQQMSYREQVLHKQLTRILGVPDLVFLLFSFISTANNSTH ALEYVLFRPNRRYNQRISLAIPNLGNTSQQEYKVSSVPNTSQSYAKVIKEHGTDFFDKDGVMKDIRAIYQVYNALQEKVQ AVCADVEKSERVVESCQAEVNKLRRQITQRKNEKEQERRLQQAVLSRQMPSESLDPAFSPRMPSSGFAAEGRSTLGDAEA SDPPPPYSDFHPNNQESTLSHSRMERSVFMPRPQAVGSSNYASTSAGLKYPGSGADLPPPQRAAGDSGEDSDDSDYENLI DPTEPSNSEYSHSKDSRPMAHPDEDPRNTQTSQI Q15018 Lys-63-specific deubiquitinase BRCC36 Homo sapiens 0.038417402 2 Trichoplusia ni LEVO MHHHHHHVDENLYFQGGGRMAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMRT VAEKVDAVRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAM YQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSESLHGPRDFWSSSQHISIEGQKEEERYERIEIPIHIVPH VTIGKVCLESAVELPKILCQEEQDAYRRIHSLTHLDSVTKIHNGSVFTKNLCSQMSAVSGPLLQWLEDRLEQNQQHLQEL QQEKEELMQELSSLE P46736 3.4.19.- BRISC and BRCA1-A complex member 2 Homo sapiens 0.045890949 2 Trichoplusia ni LEVO MHHHHHHVDENLYFQGGGRMSPEVALNRISPMLSPFISSVVRNGKVGLDATNCLRITDLKSGCTSLTPGPNCDRFKLHIP YAGETLKWDIIFNAQYPELPPDFIFGEDAEFLPDPSALQNLASWNPSNPECLLLVVKELVQQYHQFQCSRLRESSRLMFE YQTLLEEPQYGENMEIYAGKKNNWTGEFSARFLLKLPVDFSNIPTYLLKDVNEDPGEDVALLSVSFEDTEATQVYPKLYL SPRIEHALGGSSALHIPAFPGGGCLIDYVPQVCHLLTNKVQYVIQGYHKRREYIAAFLSHFGTGVVEYDAEGFTKLTLLL MWKDFCFLVHIDLPLFFPRDQPTLTFQSVYHFTNSGQLYSQAQKNYPYSPRWDGNEMAKRAKAYFKTFVPQFQEAAFANG KL Q9NXR7 BRISC and BRCA1-A complex member 1 Homo sapiens 0.039263823999999996 2 Trichoplusia ni LEVO MASWSHPQFEKVDENLYFQGGGRMEVAEPSSPTEEEEEEEEHSAEPRPRTRSNPEGAEDRAVGAQASVGSRSEGEGEAAS ADDGSLNTSGAGPKSWQVPPPAPEVQIRTPRVNCPEKVIICLDLSEEMSLPKLESFNGSKTNALNVSQKMIEMFVRTKHK IDKSHEFALVVVNDDTAWLSGLTSDPRELCSCLYDLETASCSTFNLEGLFSLIQQKTELPVTENVQTIPPPYVVRTILVY SRPPCQPQFSLTEPMKKMFQCPYFFFDVVYIHNGTEEKEEEMSWKDMFAFMGSLDTKGTSYKYEVALAGPALELHNCMAK LLAHPLQRPCQSHASYSLLEEEDEAIEVEATV Q9NWV8 Serine hydroxymethyltransferase, mitochondrial Homo sapiens 0.056144711 2 Escherichia coli BL21(DE3) LEVO MGSSHHHHHHSSGLVPRGSGQLVRMAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASE NFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQP HDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARM REVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGTRSGLIFYRKGVKAVDPKTGREIPYTFEDRINF AVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAE RVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSE TSQRLANLRQRVEQFARAFPMPGFDEH P34897 2.1.2.1 ZINC ION 6.5409e-05 2 ZN water 1.8015e-05 2 HOH singleParticle particle 0.44 7.4 50.0 HEPES 150.0 NaCl sodium chloride 0.2 TCEP Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 300 PLASMA CLEANING 12 OTHER ETHANE 80 277 LEICA EM GP

A 4 ul sample was applied to the grid and a protocol consisting of 30 s pre-blot incubation, 2 s blotting and no post-blot incubation was utilized for vitrification..

Sample was purified by gel filtration over a Superose 6 column.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 0.0 0.5 5.0 130000.0 58140.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN CEOS Cs-corrector GIF Quantum LS 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 4-20 1822 7.0 45.0 1

Drift correction was performed using Motioncor2. CTF was fitted using GCTF CryoFLARE was used for automation.

332598

Particles were auto-picked.

Initial model was generated without symmetry within RELION

1 C2 FOURIER SPACE 3.9 FSC 0.143 CUT-OFF RELION 2.1 35595 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 3 14794.0 RELION 2.1 6GVW PDB experimental model 5V7I A PDB experimental model FLEXIBLE FIT

Initial fitting with done using COOT, Rosetta was used for amino acid sequence threading and flexible fitting. COOT and ISOLDE were used for local rebuilding. Phenix was used for atom displacement parameter (ADP / B-factor) refinement.

Correlation coefficient and REAL 117.0 emd_0132_msk_1.map emd_0132_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 301.0 301.0 301.0 90.0 90.0 90.0 X Y Z -0.015580896 0.03375324 0.000060855447 0.0021443598 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-0132:::: Half map 1: unfiltered and unsharpened emd_0132_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 301.0 301.0 301.0 90.0 90.0 90.0 X Y Z -0.015033157 0.03460343 0.00006500973 0.002173768 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-0132:::: Half map 1: unfiltered and unsharpened emd_0132_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 301.0 301.0 301.0 90.0 90.0 90.0 X Y Z -0.036671966 0.06243024 0.0000539947 0.002223487 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-0132:::: Half map 1 sharpened: filtered and sharpened in the same manner as the final combined map emd_0132_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 350 350 350 0 0 0 350 350 350 301.0 301.0 301.0 90.0 90.0 90.0 X Y Z -0.034036245 0.06780611 0.00005104676 0.0022147004 0.86 0.86 0.86 AUTHOR ::::EMDATABANK.org::::EMD-0132:::: Half map 2: filtered and sharpened in the same manner as the final combined map