2024-11-13 REL RCSB RCSB RCSB 2022-06-14 2022-11-30 2022-11-30 2024-11-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35 GM118080 United States Howard Hughes Medical Institute (HHMI) United States Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) Lee HG Lima CD ATPASE, ATPASE COMPLEX, UBIQUITIN, SUMO, SMT3, QUALITY CONTROL, MOTOR PROTEIN Lee HG Lemmon AA Lima CD SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Proc.Natl.Acad.Sci.USA US 120 e2213703120 e2213703120 2023 36574706 doi:10.1073/pnas.2213703120 1091-6490 0040 PNASA6 8dau FULLOVERLAP Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two Ubiquitin moieties and one unfolded Ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two Ubiquitin moieties and one unfolded Ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) 0 1 2 3 4
Composite map. Ufd1/Npl4/Cdc48 was pre-incubated with polyubiquitylated SUMO-ubiquitin-mEOS and ATP - this class represents the portion of the substrate-bound complex engaged with two folded ubiquitin moieties and one unfolded ubiquitin (state uA)
Saccharomyces cerevisiae Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) 1 1 2 3 4
overall refinement map is "uncopenB_overall_388_postprocess_masked.mrc" and associated half maps are "uncopen_overall_half1.mrc" and "uncopen_overall_half2.mrc"
Saccharomyces cerevisiae Cdc48 hexamer 1 1
focused refinement map of the Cdc48 hexamer is "uncopenB_cdc48_525_postprocess_masked.mrc" and associated half maps are "uncopenB_cdc48_half1.mrc" and "uncopenB_cdc48_half2.mrc"
Saccharomyces cerevisiae Two folded ubiqutin moieties and one unfolded ubiquitin bound to Ufd1/Npl4 1 2 3 4
focused refinement map of Npl4/polyubiquitin density is "uncopenB_tower_484_postprocess_masked.mrc" and associated half maps are "uncopenB_tower_half1.mrc" and "uncopenB_tower_half2.mrc"
Saccharomyces cerevisiae D1/D2 ATPase domains of the Cdc48 hexamer 3 1
focused refinement map of the D1/D2 ATPase domains of Cdc48 is "uncopenB_atpase_531_postprocess_masked.mrc" and associated half maps are "uncopenB_atpase_half1.mrc" and "uncopenB_atpase_half2.mrc"
Saccharomyces cerevisiae Two folded ubiqutin moieties bound to Npl4 4 2 4
focused refinement map of the upper density of Npl4/polyubiquitin is "uncopenB_ub_489_postprocess_masked.mrc" and associated half maps are "uncopenB_ub_half1.mrc" and "uncopenB_ub_half2.mrc"
Saccharomyces cerevisiae Cell division control protein 48 Saccharomyces cerevisiae 0.09238919500000001 6 Escherichia coli LEVO GSHMGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDT VLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVR KGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHP QLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEID SIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKN MKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRET VVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPEL LSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPD QIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHR QHEAEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFN DAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS P25694 3.6.4.6 Nuclear protein localization protein 4 Saccharomyces cerevisiae 0.066144336 1 Escherichia coli LEVO GSHMLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSELADRTVMDLGLKHGDMLILN YSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKE YHEKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHV EFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDVEQVKNEMLQIDRQAQEM GLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDIS SYQVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTET NSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWE ESLLKLVSSAGWQTLVMILQESG P33755 Ubiquitin fusion degradation protein 1 Saccharomyces cerevisiae 0.040001449 1 Escherichia coli LEVO GSMFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGR VTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDD VIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYKALKAQQDKEKKNSFGKGQVLDPSVLGQGSM STRIDYAGIANSSRNKLSKFVGQGQNISGKAPKAEPKQDIKDMKITFDGEPAKLDLPEGQLFFGFPMVLPKEDEESAAGS KSSEQNFQGQGISLRKSNKRKTKSDHDSSKSKAPKSPEVIEID P53044 Ubiquitin Saccharomyces cerevisiae 0.008568769
ubiquitin that is part of the SUMO-ubiquitin(K48polyUb)-mEOS substrate; SUMO-ubiquitin-mEOS modified on K48 of Ub with a K48-linked polyubiquitin. Sequence of the unmodified substrate is MGSSHHHHHHSSGENLYFQGHMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSHMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMSAIKPDMKIKLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAKYPDNIQDYFKQSFPKGYSWERSLTFEDGGICNARNDITMEGDTFYNKVRFYGTNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDIEMALLLEGNAHYRCDFRTTYKAKEKGVKLPGAHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDNARR
3 Escherichia coli LEVO MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG P0CG63 ADENOSINE-5'-TRIPHOSPHATE 0.000507181 5 ATP ADENOSINE-5'-DIPHOSPHATE 0.000427201 7 ADP ZINC ION 6.5409e-05 2 ZN singleParticle particle 2 8.0
20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
 UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE ETHANE 100 295 FEI VITROBOT MARK IV
8 s wait, 4 s blot before plunging.
Ufd1/Npl4/Cdc48 was pre-incubated with SUMO-ubiquitin(K48polyUb)-mEOS and ATP
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 2.8000000000000003 GATAN K3 (6k x 4k) 70.577 1
Ab initio model from cryosparc
 3.7 FSC 0.143 CUT-OFF 36688 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD emd_27276.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 Z Y X -23.553677 66.110100000000003 -0.016668871 1.1007812 1.064 1.064 1.064 9.5 AUTHOR composite map of the ubiquitin unfolded state 'uA' emd_27276_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.027991194 0.0569165 -0.000025708465 0.0014606381 1.064 1.064 1.064 AUTHOR focused refinement half map 1 of Npl4 and polyubiquitin density of the ubiquitin unfolded state 'uA' emd_27276_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.057052854 0.101627134 0.0000127700905 0.0007294505 1.064 1.064 1.064 AUTHOR post-processed focused refinement map of Npl4 and polyubiquitin density of the ubiquitin unfolded state 'uA' emd_27276_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.03912591 0.07069725 0.00000044810247 0.0040617194 1.064 1.064 1.064 AUTHOR focused refinement half map 1 of Cdc48 of the ubiquitin unfolded state 'uA' emd_27276_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.06506077 0.10568066 0.00009737244 0.00150291 1.064 1.064 1.064 AUTHOR post-processed focused refinement map of the D1/D2 domains of Cdc48 of the ubiquitin unfolded state 'uA' emd_27276_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.050306544 0.097813204 0.000022018712 0.0009324229 1.064 1.064 1.064 AUTHOR post-processed focused refinement map of the central Ufd1/Npl4/polyubiquitin density of the ubiquitin unfolded state 'uA' emd_27276_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.060708694 0.101894 0.00012278465 0.0015265525 1.064 1.064 1.064 AUTHOR post-processed focused refinement map of Cdc48 of the ubiquitin unfolded state 'uA' emd_27276_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.030762963 0.06525325 -0.000026253709 0.0026205264 1.064 1.064 1.064 AUTHOR focused refinement half map 2 of the central Ufd1/Npl4/polyubiquitin density of the ubiquitin unfolded state 'uA' emd_27276_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.043720424 0.06710114 0.00000011141798 0.0041123717 1.064 1.064 1.064 AUTHOR focused refinement half map 2 of Cdc48 of the ubiquitin unfolded state 'uA' emd_27276_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.023719432 0.05670949 -0.000025507998 0.0014435495 1.064 1.064 1.064 AUTHOR focused refinement half map 2 of Npl4/polyubiquitin density of the ubiquitin unfolded state 'uA' emd_27276_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.028868807 0.06529334 -0.000025851074 0.0025682 1.064 1.064 1.064 AUTHOR focused refinement half map 1 of the central Ufd1/Npl4/polyubiquitin density of the ubiquitin unfolded state 'uA' emd_27276_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.04064939 0.06807592 -0.0000036860486 0.004087485 1.064 1.064 1.064 AUTHOR focused refinement half map 1 of the D1/D2 domains of Cdc48 of the ubiquitin unfolded state 'uA' emd_27276_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.044139564 0.07260053 -0.000004250837 0.0041393135 1.064 1.064 1.064 AUTHOR focused refinement half map 2 of the D1/D2 domains of Cdc48 of the ubiquitin unfolded state 'uA' emd_27276_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.050024122 0.08631653 0.00014299572 0.001663474 1.064 1.064 1.064 AUTHOR overall refinement post-processed map of the ubiquitin unfolded state 'uA' emd_27276_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.048041757 0.066358924 0.0000027913495 0.004884637 1.064 1.064 1.064 AUTHOR overall refinement half map 2 of the ubiquitin unfolded state 'uA' emd_27276_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 408.576 408.576 408.576 90.0 90.0 90.0 X Y Z -0.045290615 0.06996506 0.0000030449605 0.0048417053 1.064 1.064 1.064 AUTHOR overall refinement half map 1