EMDB-63850: Focused refinement of 19S in the substrate-engaged human 26S prot...

Basic information

Entry

Database: EMDB / ID: EMD-63850

• Title: Focused refinement of 19S in the substrate-engaged human 26S proteasome bound to midnolin with RPT6 at top of spiral staircase

Sample

• Complex: 26S proteasome complexed with midnolin
  • Protein or peptide: x 18 types
• Ligand: x 4 types

• Keywords: Midnolin / 26S proteasome / Complex / HYDROLASE

Function / homology

Function:

thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / positive regulation of inclusion body assembly / proteasome accessory complex / meiosis I / integrator complex / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / negative regulation of programmed cell death / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / K63-linked deubiquitinase activity / Somitogenesis / transcription factor binding / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / proteasome binding / Impaired BRCA2 binding to RAD51 / regulation of protein catabolic process / proteasome storage granule / general transcription initiation factor binding / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / protein deubiquitination / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasome assembly / mRNA export from nucleus / enzyme regulator activity / regulation of proteasomal protein catabolic process / inclusion body / TBP-class protein binding / proteasome complex / stem cell differentiation / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / P-body / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / MAPK6/MAPK4 signaling / Degradation of CDH1 / double-strand break repair via homologous recombination / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / double-strand break repair via nonhomologous end joining / CDK-mediated phosphorylation and removal of Cdc6 / ABC-family protein mediated transport / HDR through Homologous Recombination (HRR) / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Metalloprotease DUBs / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling

Domain/homology:

: / Ubiquitin interaction motif / : / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / PSMD3-like, N-terminal TPR repeats / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome subunit Rpn10 / 26S Proteasome non-ATPase regulatory subunit 7/8 / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / Ubiquitin-interacting motif. / Proteasome/cyclosome repeat / : / 26S proteasome regulatory subunit 7, OB domain / Proteasome/cyclosome repeat / von Willebrand factor type A domain / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / : / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / PCI/PINT associated module / HEAT repeats / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase

Component:

26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / Ubiquitin C-terminal hydrolase PSMD14 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 4.14 Å
• Authors: Zhu C / Qin L / Liang L

Funding support

China, 1 items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	32171224	China

• Citation: Journal: Nat Commun / Year: 2026; Title: Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover.; Authors: Chuanda Zhu / Lu Qin / Zonglin Dai / Peng Zuo / Ao Yang / Lijun Zhong / Zhiqiang Lin / Ling Liang / ; Abstract: The 26S proteasome typically degrades proteins marked by ubiquitin chains. However, a distinct, ubiquitin-independent degradation pathway for nuclear proteins exists, mediated by the adaptor protein midnolin, yet its molecular mechanism remains poorly understood. Here, we present nine cryo-electron microscopy structures of the human 26S proteasome in complex with midnolin, which collectively delineate a near-complete catalytic cycle. Our structures reveal that midnolin binds to the proteasome via the RPN1 subunit by its C-terminal helix. Unexpectedly, its ubiquitin-like domain interacts with the RPN11 deubiquitinase in a non-catalytic role. This interaction positions the adjacent Catch domain, which is responsible for substrate binding, directly above the proteasomal entrance, potentially facilitating substrate entry into the proteasome. Furthermore, we observe four consecutive spiral staircase conformations of the AAA+ ATPase hexamer during substrate translocation. These findings provide insights into the mechanisms underlying ubiquitin-independent nuclear protein degradation and may help develop strategies for targeting nuclear proteins via direct proteasomal degradation.

History

Deposition	Mar 19, 2025	-
Header (metadata) release	Mar 25, 2026	-
Map release	Mar 25, 2026	-
Update	Apr 8, 2026	-
Current status	Apr 8, 2026	Processing site: PDBc / Status: Released

Map

• File: Download / File: emd_63850.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.85 Å

Density

Contour Level	By AUTHOR: 0.04
Minimum - Maximum	-0.104990184 - 0.22822396
Average (Standard dev.)	0.0015434177 (±0.014401917)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 306.0 Å α=β=γ: 90.0 °

Supplemental data

Half map: #2

• File: emd_63850_half_map_1.map

Half map: #1

• File: emd_63850_half_map_2.map

Sample components

Entire : 26S proteasome complexed with midnolin

• Entire: Name: 26S proteasome complexed with midnolin

Components

• Complex: 26S proteasome complexed with midnolin
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 6
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 13
  • Protein or peptide: substrate peptide
  • Protein or peptide: 26S proteasome regulatory subunit 4
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 14
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 7
  • Protein or peptide: 26S proteasome complex subunit SEM1
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 1
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 12
  • Protein or peptide: 26S proteasome regulatory subunit 7
  • Protein or peptide: 26S proteasome regulatory subunit 8
  • Protein or peptide: 26S proteasome regulatory subunit 6B
  • Protein or peptide: Proteasome 26S subunit, ATPase 6
  • Protein or peptide: 26S proteasome regulatory subunit 6A
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 11
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 3
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 8
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 4
• Ligand: ADENOSINE-5'-DIPHOSPHATE
• Ligand: ZINC ION
• Ligand: ADENOSINE-5'-TRIPHOSPHATE
• Ligand: MAGNESIUM ION

Supramolecule #1: 26S proteasome complexed with midnolin

• Supramolecule: Name: 26S proteasome complexed with midnolin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: 26S proteasome non-ATPase regulatory subunit 6

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 45.592285 KDa

Sequence

String:

MPLENLEEEG LPKNPDLRIA QLRFLLSLPE HRGDAAVRDE LMAAVRDNNM APYYEALCKS LDWQIDVDLL NKMKKANEDE LKRLDEELE DAEKNLGESE IRDAMMAKAE YLCRIGDKEG ALTAFRKTYD KTVALGHRLD IVFYLLRIGL FYMDNDLITR N TEKAKSLI EEGGDWDRRN RLKVYQGLYC VAIRDFKQAA ELFLDTVSTF TSYELMDYKT FVTYTVYVSM IALERPDLRE KV IKGAEIL EVLHSLPAVR QYLFSLYECR YSVFFQSLAV VEQEMKKDWL FAPHYRYYVR EMRIHAYSQL LESYRSLTLG YMA EAFGVG VEFIDQELSR FIAAGRLHCK IDKVNEIVET NRPDSKNWQY QETIKKGDLL LNRVQKLSRV INM

UniProtKB: 26S proteasome non-ATPase regulatory subunit 6

Macromolecule #2: 26S proteasome non-ATPase regulatory subunit 13

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 13 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 42.995359 KDa

Sequence

String:

MKDVPGFLQQ SQNSGPGQPA VWHRLEELYT KKLWHQLTLQ VLDFVQDPCF AQGDGLIKLY ENFISEFEHR VNPLSLVEII LHVVRQMTD PNVALTFLEK TREKVKSSDE AVILCKTAIG ALKLNIGDLQ VTKETIEDVE EMLNNLPGVT SVHSRFYDLS S KYYQTIGN HASYYKDALR FLGCVDIKDL PVSEQQERAF TLGLAGLLGE GVFNFGELLM HPVLESLRNT DRQWLIDTLY AF NSGNVER FQTLKTAWGQ QPDLAANEAQ LLRKIQLLCL MEMTFTRPAN HRQLTFEEIA KSAKITVNEV ELLVMKALSV GLV KGSIDE VDKRVHMTWV QPRVLDLQQI KGMKDRLEFW CTDVKSMEML VEHQAHDILT

UniProtKB: 26S proteasome non-ATPase regulatory subunit 13

Macromolecule #3: substrate peptide

• Macromolecule: Name: substrate peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 586.638 Da

Sequence

String:

AAAAAAAA

Macromolecule #4: 26S proteasome regulatory subunit 4

• Macromolecule: Name: 26S proteasome regulatory subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 49.260504 KDa

Sequence

String:

MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL KLLKLERIKD YLLMEEEFIR NQEQMKPLE EKQEEERSKV DDLRGTPMSV GTLEEIIDDN HAIVSTSVGS EHYVSILSFV DKDLLEPGCS VLLNHKVHAV I GVLMDDTD PLVTVMKVEK APQETYADIG GLDNQIQEIK ESVELPLTHP EYYEEMGIKP PKGVILYGPP GTGKTLLAKA VA NQTSATF LRVVGSELIQ KYLGDGPKLV RELFRVAEEH APSIVFIDEI DAIGTKRYDS NSGGEREIQR TMLELLNQLD GFD SRGDVK VIMATNRIET LDPALIRPGR IDRKIEFPLP DEKTKKRIFQ IHTSRMTLAD DVTLDDLIMA KDDLSGADIK AICT EAGLM ALRERRMKVT NEDFKKSKEN VLYKKQEGTP EGLYL

UniProtKB: 26S proteasome regulatory subunit 4

Macromolecule #5: 26S proteasome non-ATPase regulatory subunit 14

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 14 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO; EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 34.488824 KDa

Sequence

String:

DRLLRLGGGM PGLGQGPPTD APAVDTAEQV YISSLALLKM LKHGRAGVPM EVMGLMLGEF VDDYTVRVID VFAMPQSGTG VSVEAVDPV FQAKMLDMLK QTGRPEMVVG WYHSHPGFGC WLSGVDINTQ QSFEALSERA VAVVVDPIQS VKGKVVIDAF R LINANMMV LGHEPRQTTS NLGHLNKPSI QALIHGLNRH YYSITINYRK NELEQKMLLN LHKKSWMEGL TLQDYSEHCK HN ESVVKEM LELAKNYNKA VEEEDKMTPE QLAIKNVGKQ DPKRHLEEHV DVLMTSNIVQ CLAAMLDTVV FK

UniProtKB: Ubiquitin C-terminal hydrolase PSMD14

Macromolecule #6: 26S proteasome non-ATPase regulatory subunit 7

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 37.086441 KDa

Sequence

String:

MPELAVQKVV VHPLVLLSVV DHFNRIGKVG NQKRVVGVLL GSWQKKVLDV SNSFAVPFDE DDKDDSVWFL DHDYLENMYG MFKKVNARE RIVGWYHTGP KLHKNDIAIN ELMKRYCPNS VLVIIDVKPK DLGLPTEAYI SVEEVHDDGT PTSKTFEHVT S EIGAEEAE EVGVEHLLRD IKDTTVGTLS QRITNQVHGL KGLNSKLLDI RSYLEKVATG KLPINHQIIY QLQDVFNLLP DV SLQEFVK AFYLKTNDQM VVVYLASLIR SVVALHNLIN NKIANRDAEK KEGQEKEESK KDRKEDKEKD KDKEKSDVKK EEK KEKK

UniProtKB: 26S proteasome non-ATPase regulatory subunit 7

Macromolecule #7: 26S proteasome complex subunit SEM1

• Macromolecule: Name: 26S proteasome complex subunit SEM1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 8.284611 KDa

Sequence

String:

MSEKKQPVDL GLLEEDDEFE EFPAEDWAGL DEDEDAHVWE DNWDDDNVED DFSNQLRAEL EKHGYKMETS

UniProtKB: 26S proteasome complex subunit SEM1

Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 1

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 105.958234 KDa

Sequence

String:

MITSAAGIIS LLDEDEPQLK EFALHKLNAV VNDFWAEISE SVDKIEVLYE DEGFRSRQFA ALVASKVFYH LGAFEESLNY ALGAGDLFN VNDNSEYVET IIAKCIDHYT KQCVENADLP EGEKKPIDQR LEGIVNKMFQ RCLDDHKYKQ AIGIALETRR L DVFEKTIL ESNDVPGMLA YSLKLCMSLM QNKQFRNKVL RVLVKIYMNL EKPDFINVCQ CLIFLDDPQA VSDILEKLVK ED NLLMAYQ ICFDLYESAS QQFLSSVIQN LRTVGTPIAS VPGSTNTGTV PGSEKDSDSM ETEEKTSSAF VGKTPEASPE PKD QTLKMI KILSGEMAIE LHLQFLIRNN NTDLMILKNT KDAVRNSVCH TATVIANSFM HCGTTSDQFL RDNLEWLARA TNWA KFTAT ASLGVIHKGH EKEALQLMAT YLPKDTSPGS AYQEGGGLYA LGLIHANHGG DIIDYLLNQL KNASNDIVRH GGSLG LGLA AMGTARQDVY DLLKTNLYQD DAVTGEAAGL ALGLVMLGSK NAQAIEDMVG YAQETQHEKI LRGLAVGIAL VMYGRM EEA DALIESLCRD KDPILRRSGM YTVAMAYCGS GNNKAIRRLL HVAVSDVNDD VRRAAVESLG FILFRTPEQC PSVVSLL SE SYNPHVRYGA AMALGICCAG TGNKEAINLL EPMTNDPVNY VRQGALIASA LIMIQQTEIT CPKVNQFRQL YSKVINDK H DDVMAKFGAI LAQGILDAGG HNVTISLQSR TGHTHMPSVV GVLVFTQFWF WFPLSHFLSL AYTPTCVIGL NKDLKMPKV QYKSNCKPST FAYPAPLEVP KEKEKEKVST AVLSITAKAK KKEKEKEKKE EEKMEVDEAE KKEEKEKKKE PEPNFQLLDN PARVMPAQL KVLTMPETCR YQPFKPLSIG GIIILKDTSE DIEELVEPVA AHGPKIEEEE QEPEPPEPFE YIDD

UniProtKB: 26S proteasome non-ATPase regulatory subunit 1

Macromolecule #9: 26S proteasome non-ATPase regulatory subunit 12

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 12 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 52.979359 KDa

Sequence

String:

MADGGSERAD GRIVKMEVDY SATVDQRLPE CAKLAKEGRL QEVIETLLSL EKQTRTASDM VSTSRILVAV VKMCYEAKEW DLLNENIML LSKRRSQLKQ AVAKMVQQCC TYVEEITDLP IKLRLIDTLR MVTEGKIYVE IERARLTKTL ATIKEQNGDV K EAASILQE LQVETYGSME KKERVEFILE QMRLCLAVKD YIRTQIISKK INTKFFQEEN TEKLKLKYYN LMIQLDQHEG SY LSICKHY RAIYDTPCIQ AESEKWQQAL KSVVLYVILA PFDNEQSDLV HRISGDKKLE EIPKYKDLLK LFTTMELMRW STL VEDYGM ELRKGSLESP ATDVFGSTEE GEKRWKDLKN RVVEHNIRIM AKYYTRITMK RMAQLLDLSV DESEAFLSNL VVNK TIFAK VDRLAGIINF QRPKDPNNLL NDWSQKLNSL MSLVNKTTHL IAKEEMIHNL Q

UniProtKB: 26S proteasome non-ATPase regulatory subunit 12

Macromolecule #10: 26S proteasome regulatory subunit 7

• Macromolecule: Name: 26S proteasome regulatory subunit 7 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 48.700805 KDa

Sequence

String:

MPDYLGADQR KTKEDEKDDK PIRALDEGDI ALLKTYGQST YSRQIKQVED DIQQLLKKIN ELTGIKESDT GLAPPALWDL AADKQTLQS EQPLQVARCT KIINADSEDP KYIINVKQFA KFVVDLSDQV APTDIEEGMR VGVDRNKYQI HIPLPPKIDP T VTMMQVEE KPDVTYSDVG GCKEQIEKLR EVVETPLLHP ERFVNLGIEP PKGVLLFGPP GTGKTLCARA VANRTDACFI RV IGSELVQ KYVGEGARMV RELFEMARTK KACLIFFDEI DAIGGARFDD GAGGDNEVQR TMLELINQLD GFDPRGNIKV LMA TNRPDT LDPALMRPGR LDRKIEFSLP DLEGRTHIFK IHARSMSVER DIRFELLARL CPNSTGAEIR SVCTEAGMFA IRAR RKIAT EKDFLEAVNK VIKSYAKFSA TPRYMTYN

UniProtKB: 26S proteasome regulatory subunit 7

Macromolecule #11: 26S proteasome regulatory subunit 8

• Macromolecule: Name: 26S proteasome regulatory subunit 8 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 44.852121 KDa

Sequence

String:

MELEEGKAGS GLRQYYLSKI EELQLIVNDK SQNLRRLQAQ RNELNAKVRL LREELQLLQE QGSYVGEVVR AMDKKKVLVK VHPEGKFVV DVDKNIDIND VTPNCRVALR NDSYTLHKIL PNKVDPLVSL MMVEKVPDST YEMIGGLDKQ IKEIKEVIEL P VKHPELFE ALGIAQPKGV LLYGPPGTGK TLLARAVAHH TDCTFIRVSG SELVQKFIGE GARMVRELFV MAREHAPSII FM DEIDSIG SSRLEGGSGG DSEVQRTMLE LLNQLDGFEA TKNIKVIMAT NRIDILDSAL LRPGRIDRKI EFPPPNEEAR LDI LKIHSR KMNLTRGINL RKIAELMPGA SGAEVKGVCT EAGMYALRER RVHVTQEDFE MAVAKVMQKD SEKNMSIKKL WK

UniProtKB: 26S proteasome regulatory subunit 8

Macromolecule #12: 26S proteasome regulatory subunit 6B

• Macromolecule: Name: 26S proteasome regulatory subunit 6B / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 47.426141 KDa

Sequence

String:

MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY IKDEQKNLKK EFLHAQEEVK RIQSIPLVI GQFLEAVDQN TAIVGSTTGS NYYVRILSTI DRELLKPNAS VALHKHSNAL VDVLPPEADS SIMMLTSDQK P DVMYADIG GMDIQKQEVR EAVELPLTHF ELYKQIGIDP PRGVLMYGPP GCGKTMLAKA VAHHTTAAFI RVVGSEFVQK YL GEGPRMV RDVFRLAKEN APAIIFIDEI DAIATKRFDA QTGADREVQR ILLELLNQMD GFDQNVNVKV IMATNRADTL DPA LLRPGR LDRKIEFPLP DRRQKRLIFS TITSKMNLSE EVDLEDYVAR PDKISGADIN SICQESGMLA VRENRYIVLA KDFE KAYKT VIKKDEQEHE FYK

UniProtKB: 26S proteasome regulatory subunit 6B

Macromolecule #13: Proteasome 26S subunit, ATPase 6

• Macromolecule: Name: Proteasome 26S subunit, ATPase 6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 45.867027 KDa

Sequence

String:

MAIPGIPYER RLLIMADPRD KALQDYRKKL LEHKEIDGRL KELREQLKEL TKQYEKSEND LKALQSVGQI VGEVLKQLTE EKFIVKATN GPRYVVGCRR QLDKSKLKPG TRVALDMTTL TIMRYLPREV DPLVYNMSHE DPGNVSYSEI GGLSEQIREL R EVIELPLT NPELFQRVGI IPPKGCLLYG PPGTGKTLLA RAVASQLDCN FLKVVSSSIV DKYIGESARL IREMFNYARD HQ PCIIFMD EIDAIGGRRF SEGTSADREI QRTLMELLNQ MDGFDTLHRV KMIMATNRPD TLDPALLRPG RLDRKIHIDL PNE QARLDI LKIHAGPITK HGEIDYEAIV KLSDGFNGAD LRNVCTEAGM FAIRADHDFV VQEDFMKAVR KVADSKKLES KLDY KPV

UniProtKB: 26S proteasome regulatory subunit 10B

Macromolecule #14: 26S proteasome regulatory subunit 6A

• Macromolecule: Name: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 49.266457 KDa

Sequence

String:

MNLLPNIESP VTRQEKMATV WDEAEQDGIG EEVLKMSTEE IIQRTRLLDS EIKIMKSEVL RVTHELQAMK DKIKENSEKI KVNKTLPYL VSNVIELLDV DPNDQEEDGA NIDLDSQRKG KCAVIKTSTR QTYFLPVIGL VDAEKLKPGD LVGVNKDSYL I LETLPTEY DSRVKAMEVD ERPTEQYSDI GGLDKQIQEL VEAIVLPMNH KEKFENLGIQ PPKGVLMYGP PGTGKTLLAR AC AAQTKAT FLKLAGPQLV QMFIGDGAKL VRDAFALAKE KAPSIIFIDE LDAIGTKRFD SEKAGDREVQ RTMLELLNQL DGF QPNTQV KVIAATNRVD ILDPALLRSG RLDRKIEFPM PNEEARARIM QIHSRKMNVS PDVNYEELAR CTDDFNGAQC KAVC VEAGM IALRRGATEL THEDYMEGIL EVQAKKKANL QYYA

UniProtKB: 26S proteasome regulatory subunit 6A

Macromolecule #15: 26S proteasome non-ATPase regulatory subunit 11

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 11 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 47.526688 KDa

Sequence

String:

MAAAAVVEFQ RAQSLLSTDR EASIDILHSI VKRDIQENDE EAVQVKEQSI LELGSLLAKT GQAAELGGLL KYVRPFLNSI SKAKAARLV RSLLDLFLDM EAATGQEVEL CLECIEWAKS EKRTFLRQAL EARLVSLYFD TKRYQEALHL GSQLLRELKK M DDKALLVE VQLLESKTYH ALSNLPKARA ALTSARTTAN AIYCPPKLQA TLDMQSGIIH AAEEKDWKTA YSYFYEAFEG YD SIDSPKA ITSLKYMLLC KIMLNTPEDV QALVSGKLAL RYAGRQTEAL KCVAQASKNR SLADFEKALT DYRAELRDDP IIS THLAKL YDNLLEQNLI RVIEPFSRVQ IEHISSLIKL SKADVERKLS QMILDKKFHG ILDQGEGVLI IFDEPPVDKT YEAA LETIQ NMSKVVDSLY NKAKKLT

UniProtKB: 26S proteasome non-ATPase regulatory subunit 11

Macromolecule #16: 26S proteasome non-ATPase regulatory subunit 3

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 3 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.935297 KDa

Sequence

String:

KQEGSARRRG ADKAKPPPGG GEQEPPPPPA PQDVEMKEEA ATGGGSTGEA DGKTAAAAAE HSQRELDTVT LEDIKEHVKQ LEKAVSGKE PRFVLRALRM LPSTSRRLNH YVLYKAVQGF FTSNNATRDF LLPFLEEPMD TEADLQFRPR TGKAASTPLL P EVEAYLQL LVVIFMMNSK RYKEAQKISD DLMQKISTQN RRALDLVAAK CYYYHARVYE FLDKLDVVRS FLHARLRTAT LR HDADGQA TLLNLLLRNY LHYSLYDQAE KLVSKSVFPE QANNNEWARY LYYTGRIKAI QLEYSEARRT MTNALRKAPQ HTA VGFKQT VHKLLIVVEL LLGEIPDRLQ FRQPSLKRSL MPYFLLTQAV RTGNLAKFNQ VLDQFGEKFQ ADGTYTLIIR LRHN VIKTG VRMISLSYSR ISLADIAQKL QLDSPEDAEF IVAKAIRDGV IEASINHEKG YVQSKEMIDI YSTREPQLAF HQRIS FCLD IHNMSVKAMR FPPKSYNKDL ESAEERRERE QQDLEFAKEM AEDDDDSFP

UniProtKB: 26S proteasome non-ATPase regulatory subunit 3

Macromolecule #17: 26S proteasome non-ATPase regulatory subunit 8

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 8 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 39.536676 KDa

Sequence

String:

FIKGRAPRAP PRERRRATRG GLRQVVAPPR ALGSTSRPHF RRASVCRRRC RKSGGLLAAS RKMAAAAVNG AAGFSSSGPA ATSGAVLQA ATGMYEQLKG EWNRKSPNLS KCGEELGRLK LVLLELNFLP TTGTKLTKQQ LILARDILEI GAQWSILRKD I PSFERYMA QLKCYYFDYK EQLPESAYMH QLLGLNLLFL LSQNRVAEFH TELERLPAKD IQTNVYIKHP VSLEQYLMEG SY NKVFLAK GNIPAESYTF FIDILLDTIR DEIAGCIEKA YEKILFTEAT RILFFNTPKK MTDYAKKRGW VLGPNNYYSF ASQ QQKPED TTIPSTELAK QVIEYARQLE MIV

UniProtKB: 26S proteasome non-ATPase regulatory subunit 8

Macromolecule #18: 26S proteasome non-ATPase regulatory subunit 4

• Macromolecule: Name: 26S proteasome non-ATPase regulatory subunit 4 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 40.78159 KDa

Sequence

String:

MVLESTMVCV DNSEYMRNGD FLPTRLQAQQ DAVNIVCHSK TRSNPENNVG LITLANDCEV LTTLTPDTGR ILSKLHTVQP KGKITFCTG IRVAHLALKH RQGKNHKMRI IAFVGSPVED NEKDLVKLAK RLKKEKVNVD IINFGEEEVN TEKLTAFVNT L NGKDGTGS HLVTVPPGPS LADALISSPI LAGEGGAMLG LGASDFEFGV DPSADPELAL ALRVSMEEQR QRQEEEARRA AA ASAAEAG IATTGTEDSD DALLKMTISQ QEFGRTGLPD LSSMTEEEQI AYAMQMSLQG AEFGQAESAD IDASSAMDTS EPA KEEDDY DVMQDPEFLQ SVLENLPGVD PNNEAIRNAM GSLASQATKD GKKDKKEEDK K

UniProtKB: 26S proteasome non-ATPase regulatory subunit 4

Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 19 / Number of copies: 3 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Macromolecule #20: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #21: ADENOSINE-5'-TRIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 21 / Number of copies: 3 / Formula: ATP
• Molecular weight: Theoretical: 507.181 Da

Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

Macromolecule #22: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: INSILICO MODEL
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9022
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD