2024-03-13 REL RCSB RCSB RCSB 2018-08-15 2018-10-17 2018-10-17 2024-03-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-GM094497 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) DP2-EB020402 United States Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state) de la Pena AH Goodall EA 26S Proteasome, ATPase, AAA+, Protease, Motor protein, Ubiquitin de la Pena AH Goodall EA Gates SN Lander GC Martin A Substrate-engaged 26Sproteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation. Science US 362 2018 30309908 doi:10.1126/science.aav0725 1095-9203 0038 SCIEAS EMD-9043 other EM volume EMD-9044 other EM volume EMD-9045 other EM volume 6ef0 FULLOVERLAP Substrate-engaged 26S proteasome in the 1D* state Substrate-engaged 26S proteasome in the 1D* state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
Yeast 26S proteasome bound to ubiquitinated substrate in the presence of ATP
 proteasome 1 1 2 3 4 5 6 7 8 9 10 11 12 13 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c substrate 1 14 Homo sapiens Proteasome subunit alpha type-1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.026801548999999997 1 Saccharomyces cerevisiae W303 LEVO GYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYIFCISRTIGMVVNGPIPDA RNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATA TGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAI P21243 3.4.25.1 Proteasome subunit alpha type-2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.027191828 1 Saccharomyces cerevisiae W303 LEVO MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGP DYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWK ATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS QEINDRLEAL P23639 3.4.25.1 Proteasome subunit alpha type-3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.027080506 1 Saccharomyces cerevisiae W303 LEVO MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGL TADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGW KAISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV KTGI P23638 3.4.25.1 Proteasome subunit alpha type-4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.026993474999999996 1 Saccharomyces cerevisiae W303 LEVO MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNA DSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWS AQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK QE P40303 3.4.25.1 Proteasome subunit alpha type-5 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.027444868999999997 1 Saccharomyces cerevisiae W303 LEVO MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSG LTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEP SGTFYRYNAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI KELKEKEAA P32379 3.4.25.1 Proteasome subunit alpha type-6 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.025634 1 Saccharomyces cerevisiae W303 LEVO MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIKCDEHMGLSLAGLAPD ARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTA IGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI P40302 3.4.25.1 Probable proteasome subunit alpha type-7 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.027092719 1 Saccharomyces cerevisiae W303 LEVO SIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLI PDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKG AATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDF AQKEIN P21242 3.4.25.1 26S proteasome regulatory subunit 7 homolog Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.028597023 1 Saccharomyces cerevisiae W303 LEVO EEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELV QKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNT LDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATE KDFLKAVDKVISGYKKF P33299 26S proteasome regulatory subunit 4 homolog Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.030109571999999998 1 Saccharomyces cerevisiae W303 LEVO PMVSVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFL RIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVI MATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALR ERRMQVTAEDFKQAKERVMKNKVEENLEGLY P40327 26S proteasome regulatory subunit 8 homolog Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.030522594 1 Saccharomyces cerevisiae W303 LEVO ADPLVSLMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCK FIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIK IIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGMYA LRERRIHVTQEDFELAVGKVMNKNQETAISVAKLFK Q01939 26S proteasome regulatory subunit 6B homolog Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.030387692999999997 1 Saccharomyces cerevisiae W303 LEVO SISVMGENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIR VNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIM ATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVR KNRYVILQSDLEEAYATQVKTDNTVDKFDFYK P33298 26S proteasome subunit RPT4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.030386865 1 Saccharomyces cerevisiae W303 LEVO DPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANF IFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKI IMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAI RDDRDHINPDDLMKAVRKVAEVKKLEGTIEYQK P53549 26S proteasome regulatory subunit 6A Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.028497504 1 Saccharomyces cerevisiae W303 LEVO PTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQMY IGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLDP ALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVTVEAGMIALRNGQSSVKHEDF VEGISEVQARKSKSVSFY P33297 model substrate polypeptide Homo sapiens 0.001130277 1 Escherichia coli BL21 LEVO SARLGGASIAVQ ADENOSINE-5'-DIPHOSPHATE 0.000427201 3 ADP ADENOSINE-5'-TRIPHOSPHATE 0.000507181 3 ATP singleParticle particle 25 7.6 20.0 HEPES 25.0 NaCl 25.0 KCl 10.0 MgCl2 1.0 TCEP 5.0 ATP 0.05 Nonidet P-40 6.0 ortho-phenanthroline Quantifoil R2/2 COPPER 400 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 90 277 HOMEMADE PLUNGER
specimens were manually blotted with Whatman #1 filter paper.
26S proteasomes were diluted to a concentration of 20 micromolar in a buffer with an ATP regeneration system, and 6 mM ortho-phenanthroline. This solution was mixed with an equal volume of 50 micromolar ubiquitinated model substrate
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 -1.0 -1.5 -2.5 -3.0 29000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
images were acquired in nanoprobe mode
GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1-25 1 11656 6.25 50.0 1
Camera was operated in counting mode
579361
Particles were selected using the Relion template-based particle picker
 5MP9 C1 BACK PROJECTION 4.43 FSC 0.143 CUT-OFF RELION 2.1 34701 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 emd_9042.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z 0.0 0.19451101 0.0012396917 0.006442988 1.03 1.03 1.03 0.03 AUTHOR Yeast 26S proteasome bound to ubiquitinated substrate (1D* motor state) 5MPC PDB experimental model RIGID BODY FIT REAL emd_9042_msk_1.map emd_9042_msk_2.map emd_9042_msk_3.map emd_9042_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.029265495 0.053098757 0.0002084411 0.003898115 1.03 1.03 1.03 AUTHOR Global (half 1) emd_9042_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.0224508 0.045008905 0.00020879738 0.0029136648 1.03 1.03 1.03 AUTHOR Alpha ring (half 1) emd_9042_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.087010354 0.14254998 0.00041440426 0.00810314 1.03 1.03 1.03 AUTHOR Global (sharpened) emd_9042_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.07709109 0.13274275 0.00041447964 0.0067590154 1.03 1.03 1.03 AUTHOR Alpha ring (sharpened) emd_9042_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.028757814 0.050015993 0.00020616363 0.003435828 1.03 1.03 1.03 AUTHOR Motor (half 2) emd_9042_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.021857819 0.044247307 0.00020568226 0.002918476 1.03 1.03 1.03 AUTHOR Alpha ring (half 2) emd_9042_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.02612318 0.05488757 0.00020861615 0.0034318357 1.03 1.03 1.03 AUTHOR Motor (half 1) emd_9042_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.030409735 0.050075356 0.00020596317 0.003915895 1.03 1.03 1.03 AUTHOR Global (half 2) emd_9042_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 350.19998 350.19998 350.19998 90.0 90.0 90.0 X Y Z -0.07578235 0.13513236 0.0004147798 0.0066970503 1.03 1.03 1.03 AUTHOR Motor (sharpened)