Structure of apo BRCA1-A complex in presence of K63-oligoUbATA

2026-08-19 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _em_admin.last_update PDBe PDBe 2025-09-09 2026-07-08 2026-07-08 2026-08-19 Oncode Institute Netherlands Netherlands Organisation for Scientific Research (NWO) OCENW.M.21.288 Netherlands Structure of apo BRCA1-A complex in presence of K63-oligoUbATA Murachelli AG Sixma TK Deubiquitinase; DNA repair; Metalloprotein; Ubiquitin chains;, METAL BINDING PROTEIN Murachelli AG El Oualid F Sixma TK A ubiquitin chain-feeding mechanism for BRCA1-A. Nat Commun UK 17 2026 42581048 doi:10.1038/s41467-026-75797-w 2041-1723 Murachelli AG El Oualid F Sixma TK A ubiquitin chain-feeding mechanism for BRCA1-A Biorxiv US 2026 doi:10.64898/2026.06.05.730370 2692-8205 9smr FULLOVERLAP PDB 9SMN unspecified PDB 9SMP unspecified EMDB EMD-55040 associated EM volume

BRCA1-A complex without substrate in the active sites BRCA1-A complex without substrate in the active sites 0 1 2 3 4 5

"Synthetic, non-cleavable Lys63-linked polyubiquitin chains were included in the sample, but the complex did not engage them."

Homo sapiens 0.454 BRCA1-A complex subunit Abraxas 1 Homo sapiens 0.046731754 2 Spodoptera frugiperda LEVO MEGESTSAVLSGFVLGALAFQHLNTDSDTEGFLLGEVKGEAKNSITDSQMDDVEVVYTIDIQKYIPCYQLFSFYNSSGEV NEQALKKILSNVKKNVVGWYKFRRHSDQIMTFRERLLHKNLQEHFSNQDLVFLLLTPSIITESCSTHRLEHSLYKPQKGL FHRVPLVVANLGMSEQLGYKTVSGSCMSTGFSRAVQTHSSKFFEEDGSLKEVHKINEMYASLQEELKSICKKVEDSEQAV DKLVKDVNRLKREIEKRRGAQIQAAREKNIQKDPQENIFLCQALRTFFPNSEFLHSCVMSLKNRHVSKSSCNYNHHLDVV DNLTLMVEHTDIPEASPASTPQIIKHKALDLDDRWQFKRSRLLDTQDKRSKADTGSSNQDKASKMSSPETDEEIEKMKGF GEYSRSPTF Q6UWZ7 Lys-63-specific deubiquitinase BRCC36 Homo sapiens 0.036119917999999994 2 Spodoptera frugiperda LEVO MAVQVVQAVQAVHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMRTVAEKVDAVRIVHIHSVIIL RRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIED KNTKTGRVLYTCFQSIQAQKSSESLHGPRDFWSSSQHISIEGQKEEERYERIEIPIHIVPHVTIGKVCLESAVELPKILC QEEQDAYRRIHSLTHLDSVTKIHNGSVFTKNLCSQMSAVSGPLLQWLEDRLEQNQQHLQELQQEKEELMQELSSLE P46736 3.4.19.- BRISC and BRCA1-A complex member 2 Homo sapiens 0.043593472999999994 2 Spodoptera frugiperda LEVO MSPEVALNRISPMLSPFISSVVRNGKVGLDATNCLRITDLKSGCTSLTPGPNCDRFKLHIPYAGETLKWDIIFNAQYPEL PPDFIFGEDAEFLPDPSALQNLASWNPSNPECLLLVVKELVQQYHQFQCSRLRESSRLMFEYQTLLEEPQYGENMEIYAG KKNNWTGEFSARFLLKLPVDFSNIPTYLLKDVNEDPGEDVALLSVSFEDTEATQVYPKLYLSPRIEHALGGSSALHIPAF PGGGCLIDYVPQVCHLLTNKVQYVIQGYHKRREYIAAFLSHFGTGVVEYDAEGFTKLTLLLMWKDFCFLVHIDLPLFFPR DQPTLTFQSVYHFTNSGQLYSQAQKNYPYSPRWDGNEMAKRAKAYFKTFVPQFQEAAFANGKL Q9NXR7 BRISC and BRCA1-A complex member 1 Homo sapiens 0.038796379 2 Spodoptera frugiperda LEVO MAHHHHHHSAALEVLFQGPGMEVAEPSSPTEEEEEEEEHSAEPRPRTRSNPEGAEDRAVGAQASVGSRSEGEGEAASADD GSLNTSGAGPKSWQVPPPAPEVQIRTPRVNCPEKVIICLDLSEEMSLPKLESFNGSKTNALNVSQKMIEMFVRTKHKIDK SHEFALVVVNDDTAWLSGLTSDPRELCSCLYDLETASCSTFNLEGLFSLIQQKTELPVTENVQTIPPPYVVRTILVYSRP PCQPQFSLTEPMKKMFQCPYFFFDVVYIHNGTEEKEEEMSWKDMFAFMGSLDTKGTSYKYEVALAGPALELHNCMAKLLA HPLQRPCQSHASYSLLEEEDEAIEVEATV Q9NWV8 BRCA1-A complex subunit RAP80 Homo sapiens 0.01915817

StrepII tagged

2 Spodoptera frugiperda LEVO MASWSHPQFEKGALEVLFQGPGKGLQDTGGTVNYFWGIPFCPDGVDPNQYTKVILCQLEVYQKSLKMAQRQLLNKKGFGE PVLPRPPSLIQNECGQGEQASEKNECISEDMGDEDKEERQESRASDWHSKTKDFQESSIKSLKEKLLLEEEPTTSHGQSS QGIVEETSEEG Q96RL1 ZINC ION 6.5409e-05 2 ZN water 1.8015e-05 2 HOH singleParticle particle 0.33 8.0 150.0 NaCl Sodium Chloride 20.0 C8H18N2O4S 2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid (HEPES) 0.05 C14H28O6 Octyl beta-D-glucopyranoside (Octyl glucoside) 2.0 C9H15O6P tris(2-carboxyethyl)phosphine (TCEP)

0.5% octyl-glucoside, 150 mM NaCl, 20 mM HEPES, pH 8.0 buffer was added as 10x to protein in 150 mM NaCl, 20 mM HEPES pH 8.0 prior to grid freezing.

Quantifoil R2/2 COPPER 300 CARBON HOLEY ARRAY GLOW DISCHARGE 60 AIR 0.02

Current: 30 mA

ETHANE 100 277 FEI VITROBOT MARK IV

Blot time: 5 s Blot Force: 0.

3.3 mg/ml of BRCA1-A complex were mixed with 1 ul of uncleavable K63-linked ubiquitin chains (concentration > 10 uM - see paper), and incubated at 37C for 15 minutes; Octyl glucoside was added at 10X concentration prior to freezing. Bound ubiquitin is present at the wrist site, but not in either active site.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.2 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 4623 3.88 50.0

Four shots per hole, at quadrant positions (particle number was low in the centre owing to lensing effects)

1 647888

Clean particles.

cryoSPARC 4 PHASE FLIPPING AND AMPLITUDE CORRECTION

Model was created ab-initio from picked particles

1 C1 3.25 FSC 0.143 CUT-OFF cryoSPARC 4

Maasked resolution. For unmasked resolution see FSC plot in this deposition.

279338 MAXIMUM LIKELIHOOD cryoSPARC 4 MAXIMUM LIKELIHOOD cryoSPARC 4 2 310000.0 cryoSPARC 4

This deposition refers to the open state of the complex. There is a closed state in the ensemble, see related depositions.

emd_55040.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 551.7936 551.7936 551.7936 90.0 90.0 90.0 X Y Z -0.15822725 0.42076582 -0.000075066826 0.0046755136 1.2773 1.2773 1.2773 0.015 AUTHOR ::::EMDATABANK.org::::EMD-55040:::: Apo-BRCA1-A complex 9SMN PDB experimental model FLEXIBLE FIT

Starting model was fitted with coot and refined with Phenix real space refine and Refmac Servalcat.

REAL emd_55040_msk_1.map emd_55040_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 551.7936 551.7936 551.7936 90.0 90.0 90.0 X Y Z -2.6858914 193.813639999999992 0.0035660595 1.051988 1.2773 1.2773 1.2773 AUTHOR ::::EMDATABANK.org::::EMD-55040:::: deepEMhancer-sharpened map emd_55040_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 551.7936 551.7936 551.7936 90.0 90.0 90.0 X Y Z -0.1886893 0.44769567 -0.000002927181 0.008355598 1.2773 1.2773 1.2773 AUTHOR ::::EMDATABANK.org::::EMD-55040:::: emd_55040_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 551.7936 551.7936 551.7936 90.0 90.0 90.0 X Y Z -0.18221498 0.4517393 -0.0000032079688 0.008314891 1.2773 1.2773 1.2773 AUTHOR ::::EMDATABANK.org::::EMD-55040::::