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- EMDB-8683: Conformational Landscape of the p28-Bound Human Proteasome Regula... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8683 | |||||||||
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Title | Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle | |||||||||
![]() | Final Map of Rpn1-p28-AAA subcomplex in the TA7 state, corrected with a B-factor of -400 | |||||||||
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![]() | p28 / 26S proteasome / regulatory particle / 19S / gankyrin / HYDROLASE | |||||||||
Function / homology | ![]() cytoplasmic sequestering of NF-kappaB / positive regulation of inclusion body assembly / proteasome regulatory particle assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome-activating activity ...cytoplasmic sequestering of NF-kappaB / positive regulation of inclusion body assembly / proteasome regulatory particle assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / intermediate filament cytoskeleton / Somitogenesis / negative regulation of NF-kappaB transcription factor activity / negative regulation of MAPK cascade / regulation of protein catabolic process / negative regulation of release of cytochrome c from mitochondria / proteasome storage granule / negative regulation of DNA damage response, signal transduction by p53 class mediator / transcription factor binding / blastocyst development / positive regulation of cyclin-dependent protein serine/threonine kinase activity / general transcription initiation factor binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / enzyme regulator activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / ERAD pathway / inclusion body / cytoskeletal protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / protein localization to plasma membrane / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / P-body / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / cytoplasmic ribonucleoprotein granule / Regulation of RAS by GAPs / osteoblast differentiation / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / protein-macromolecule adaptor activity / ER-Phagosome pathway / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / positive regulation of cell growth / proteasome-mediated ubiquitin-dependent protein catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.7 Å | |||||||||
![]() | Lu Y / Wu J | |||||||||
![]() | ![]() Title: Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle. Authors: Ying Lu / Jiayi Wu / Yuanchen Dong / Shuobing Chen / Shuangwu Sun / Yong-Bei Ma / Qi Ouyang / Daniel Finley / Marc W Kirschner / Youdong Mao / ![]() ![]() Abstract: The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of ...The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 81.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.9 KB 20.9 KB | Display Display | ![]() |
Images | ![]() | 66.8 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vhrMC ![]() 8672C ![]() 8674C ![]() 8675C ![]() 8676C ![]() 8677C ![]() 8678C ![]() 8679C ![]() 8680C ![]() 8681C ![]() 8682C ![]() 8684C ![]() 5vgzC ![]() 5vhfC ![]() 5vhhC ![]() 5vhiC ![]() 5vhjC ![]() 5vhmC ![]() 5vhnC ![]() 5vhoC ![]() 5vhpC ![]() 5vhqC ![]() 5vhsC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 70.0 Data #1: Classified single-particle datasets for multiple conformations of p28-bound human regulatory complex [picked particles - multiframe - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Final Map of Rpn1-p28-AAA subcomplex in the TA7 state, corrected with a B-factor of -400 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Proteasome regulatory particle
Entire | Name: Proteasome regulatory particle |
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Components |
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-Supramolecule #1: Proteasome regulatory particle
Supramolecule | Name: Proteasome regulatory particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: 26S proteasome non-ATPase regulatory subunit 10
Macromolecule | Name: 26S proteasome non-ATPase regulatory subunit 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.14249 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: CVSNLMVCNL AYSGKLEELK ESILADKSLA TRTDQDSRTA LHWACSAGHT EIVEFLLQLG VPVNDKDDAG WSPLHIAASA GRDEIVKAL LGKGAQVNAV NQNGCTPLHY AASKNRHEIA VMLLEGGANP DAKDHYEATA MHRAAAKGNL KMIHILLYYK A STNIQDTE ...String: CVSNLMVCNL AYSGKLEELK ESILADKSLA TRTDQDSRTA LHWACSAGHT EIVEFLLQLG VPVNDKDDAG WSPLHIAASA GRDEIVKAL LGKGAQVNAV NQNGCTPLHY AASKNRHEIA VMLLEGGANP DAKDHYEATA MHRAAAKGNL KMIHILLYYK A STNIQDTE GNTPLHLACD EERVEEAKLL VSQGASIYIE NKEEKTPLQV AKGGLGLILK RMVEG UniProtKB: 26S proteasome non-ATPase regulatory subunit 10 |
-Macromolecule #2: 26S proteasome regulatory subunit 7
Macromolecule | Name: 26S proteasome regulatory subunit 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.746465 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: PTVTMMQVEE KPDVTYSDVG GCKEQIEKLR EVVETPLLHP ERFVNLGIEP PKGVLLFGPP GTGKTLCARA VANRTDACFI RVIGSELVQ KYVGEGARMV RELFEMARTK KACLIFFDEI DAIGGARFDD GAGGDNEVQR TMLELINQLD GFDPRGNIKV L MATNRPDT ...String: PTVTMMQVEE KPDVTYSDVG GCKEQIEKLR EVVETPLLHP ERFVNLGIEP PKGVLLFGPP GTGKTLCARA VANRTDACFI RVIGSELVQ KYVGEGARMV RELFEMARTK KACLIFFDEI DAIGGARFDD GAGGDNEVQR TMLELINQLD GFDPRGNIKV L MATNRPDT LDPALMRPGR LDRKIEFSLP DLEGRTHIFK IHARSMSVER DIRFELLARL CPNSTGAEIR SVCTEAGMFA IR ARRKIAT EKDFLEAVNK VIKSYAKFS UniProtKB: 26S proteasome regulatory subunit 7 |
-Macromolecule #3: 26S proteasome regulatory subunit 4
Macromolecule | Name: 26S proteasome regulatory subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.958395 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: TDPLVTVMKV EKAPQETYAD IGGLDNQIQE IKESVELPLT HPEYYEEMGI KPPKGVILYG PPGTGKTLLA KAVANQTSAT FLRVVGSEL IQKYLGDGPK LVRELFRVAE EHAPSIVFID EIDAIGTKRY DSNSGGEREI QRTMLELLNQ LDGFDSRGDV K VIMATNRI ...String: TDPLVTVMKV EKAPQETYAD IGGLDNQIQE IKESVELPLT HPEYYEEMGI KPPKGVILYG PPGTGKTLLA KAVANQTSAT FLRVVGSEL IQKYLGDGPK LVRELFRVAE EHAPSIVFID EIDAIGTKRY DSNSGGEREI QRTMLELLNQ LDGFDSRGDV K VIMATNRI ETLDPALIRP GRIDRKIEFP LPDEKTKKRI FQIHTSRMTL ADDVTLDDLI MAKDDLSGAD IKAICTEAGL MA LRERRMK VTNEDFKKSK ENVLYKKQEG UniProtKB: 26S proteasome regulatory subunit 4 |
-Macromolecule #4: 26S proteasome regulatory subunit 6B
Macromolecule | Name: 26S proteasome regulatory subunit 6B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.497975 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: PEADSSIMML TSDQKPDVMY ADIGGMDIQK QEVREAVELP LTHFELYKQI GIDPPRGVLM YGPPGCGKTM LAKAVAHHTT AAFIRVVGS EFVQKYLGEG PRMVRDVFRL AKENAPAIIF IDEIDAIATK RFDAQTGADR EVQRILLELL NQMDGFDQNV N VKVIMATN ...String: PEADSSIMML TSDQKPDVMY ADIGGMDIQK QEVREAVELP LTHFELYKQI GIDPPRGVLM YGPPGCGKTM LAKAVAHHTT AAFIRVVGS EFVQKYLGEG PRMVRDVFRL AKENAPAIIF IDEIDAIATK RFDAQTGADR EVQRILLELL NQMDGFDQNV N VKVIMATN RADTLDPALL RPGRLDRKIE FPLPDRRQKR LIFSTITSKM NLSEEVDLED YVARPDKISG ADINSICQES GM LAVRENR YIVLAKDFEK AYKTV UniProtKB: 26S proteasome regulatory subunit 6B |
-Macromolecule #5: 26S proteasome regulatory subunit 10B
Macromolecule | Name: 26S proteasome regulatory subunit 10B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.434889 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GNVSYSEIGG LSEQIRELRE VIELPLTNPE LFQRVGIIPP KGCLLYGPPG TGKTLLARAV ASQLDCNFLK VVSSSIVDKY IGESARLIR EMFNYARDHQ PCIIFMDEID AIGGRRFSEG TSADREIQRT LMELLNQMDG FDTLHRVKMI MATNRPDTLD P ALLRPGRL ...String: GNVSYSEIGG LSEQIRELRE VIELPLTNPE LFQRVGIIPP KGCLLYGPPG TGKTLLARAV ASQLDCNFLK VVSSSIVDKY IGESARLIR EMFNYARDHQ PCIIFMDEID AIGGRRFSEG TSADREIQRT LMELLNQMDG FDTLHRVKMI MATNRPDTLD P ALLRPGRL DRKIHIDLPN EQARLDILKI HAGPITKHGE IDYEAIVKLS DGFNGADLRN VCTEAGMFAI RADHDFVVQE DF MKAVRKV ADSKKLESKL DYKPV UniProtKB: 26S proteasome regulatory subunit 10B |
-Macromolecule #6: 26S proteasome regulatory subunit 6A
Macromolecule | Name: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.773246 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: TEYDSRVKAM EVDERPTEQY SDIGGLDKQI QELVEAIVLP MNHKEKFENL GIQPPKGVLM YGPPGTGKTL LARACAAQTK ATFLKLAGP QLVQMFIGDG AKLVRDAFAL AKEKAPSIIF IDELDAIGTK RFDSEKAGDR EVQRTMLELL NQLDGFQPNT Q VKVIAATN ...String: TEYDSRVKAM EVDERPTEQY SDIGGLDKQI QELVEAIVLP MNHKEKFENL GIQPPKGVLM YGPPGTGKTL LARACAAQTK ATFLKLAGP QLVQMFIGDG AKLVRDAFAL AKEKAPSIIF IDELDAIGTK RFDSEKAGDR EVQRTMLELL NQLDGFQPNT Q VKVIAATN RVDILDPALL RSGRLDRKIE FPMPNEEARA RIMQIHSRKM NVSPDVNYEE LARCTDDFNG AQCKAVCVEA GM IALRRGA TELTHEDYME GILEVQAKKK UniProtKB: 26S proteasome regulatory subunit 6A |
-Macromolecule #7: 26S proteasome regulatory subunit 8
Macromolecule | Name: 26S proteasome regulatory subunit 8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 29.501363 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK EIKEVIELPV KHPELFEALG IAQPKGVLLY GPPGTGKTLL ARAVAHHTDC TFIRVSGSE LVQKFIGEGA RMVRELFVMA REHAPSIIFM DEIDSIGSSR LEGGSGGDSE VQRTMLELLN QLDGFEATKN I KVIMATNR ...String: KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK EIKEVIELPV KHPELFEALG IAQPKGVLLY GPPGTGKTLL ARAVAHHTDC TFIRVSGSE LVQKFIGEGA RMVRELFVMA REHAPSIIFM DEIDSIGSSR LEGGSGGDSE VQRTMLELLN QLDGFEATKN I KVIMATNR IDILDSALLR PGRIDRKIEF PPPNEEARLD ILKIHSRKMN LTRGINLRKI AELMPGASGA EVKGVCTEAG MY ALRERRV HVTQEDFEMA VAKVMQKDS UniProtKB: 26S proteasome regulatory subunit 8 |
-Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 2
Macromolecule | Name: 26S proteasome non-ATPase regulatory subunit 2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93.790188 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: RDKAPVQPQQ SPAAAPGGTD EKPSGKERRD AGDKDKEQEL SEEDKQLQDE LEMLVERLGE KDTSLYRPAL EELRRQIRSS TTSMTSVPK PLKFLRPHYG KLKEIYENMA PGENKRFAAD IISVLAMTMS GERECLKYRL VGSQEELASW GHEYVRHLAG E VAKEWQEL ...String: RDKAPVQPQQ SPAAAPGGTD EKPSGKERRD AGDKDKEQEL SEEDKQLQDE LEMLVERLGE KDTSLYRPAL EELRRQIRSS TTSMTSVPK PLKFLRPHYG KLKEIYENMA PGENKRFAAD IISVLAMTMS GERECLKYRL VGSQEELASW GHEYVRHLAG E VAKEWQEL DDAEKVQREP LLTLVKEIVP YNMAHNAEHE ACDLLMEIEQ VDMLEKDIDE NAYAKVCLYL TSCVNYVPEP EN SALLRCA LGVFRKFSRF PEALRLALML NDMELVEDIF TSCKDVVVQK QMAFMLGRHG VFLELSEDVE EYEDLTEIMS NVQ LNSNFL ALARELDIME PKVPDDIYKT HLENNRFGGS GSQVDSARMN LASSFVNGFV NAAFGQDKLL TDDGNKWLYK NKDH GMLSA AASLGMILLW DVDGGLTQID KYLYSSEDYI KSGALLACGI VNSGVRNECD PALALLSDYV LHNSNTMRLG SIFGL GLAY AGSNREDVLT LLLPVMGDSK SSMEVAGVTA LACGMIAVGS CNGDVTSTIL QTIMEKSETE LKDTYARWLP LGLGLN HLG KGEAIEAILA ALEVVSEPFR SFANTLVDVC AYAGSGNVLK VQQLLHICSE HFDSKEKEED KDKKEKKDKD KKEAPAD MG AHQGVAVLGI ALIAMGEEIG AEMALRTFGH LLRYGEPTLR RAVPLALALI SVSNPRLNIL DTLSKFSHDA DPEVSYNS I FAMGMVGSGT NNARLAAMLR QLAQYHAKDP NNLFMVRLAQ GLTHLGKGTL TLCPYHSDRQ LMSQVAVAGL LTVLVSFLD VRNIILGKSH YVLYGLVAAM QPRMLVTFDE ELRPLPVSVR VGQAVDVV UniProtKB: 26S proteasome non-ATPase regulatory subunit 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14464 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |