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- EMDB-63775: Focused refinement of RPN1 and the C-terminal helix of midnolin i... -

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Basic information

Entry
Database: EMDB / ID: EMD-63775
TitleFocused refinement of RPN1 and the C-terminal helix of midnolin in the substrate-engaged human 26S proteasome
Map data
Sample
  • Complex: 26S proteasome complexed with midnolin
    • Complex: midnolin
      • Complex: 26S proteasome
        • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 2
      • Protein or peptide: Midnolin
KeywordsMidnolin / 26S proteasome / Complex / HYDROLASE
Function / homology
Function and homology information


negative regulation of glucokinase activity / proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / regulation of protein catabolic process / proteasome storage granule ...negative regulation of glucokinase activity / proteasome accessory complex / proteasome regulatory particle / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / regulation of protein catabolic process / proteasome storage granule / proteasomal ubiquitin-independent protein catabolic process / enzyme regulator activity / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / negative regulation of insulin secretion / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / kinase binding / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / Neddylation / secretory granule lumen / molecular adaptor activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / Neutrophil degranulation / nucleolus / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Midnolin / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Armadillo-like helical / Ubiquitin family ...Midnolin / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 2 / Midnolin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsZhu C / Qin L / Liang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171224 China
CitationJournal: To Be Published
Title: Molecular basis for ubiquitin-independent substrate degradation by midnolin-proteasome
Authors: Zhu C / Qin L
History
DepositionMar 17, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63775.png

Downloads & links

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Map

FileDownload / File: emd_63775.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.7493661 - 1.1964312
Average (Standard dev.)-0.0000018800816 (±0.033130396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63775_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63775_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 26S proteasome complexed with midnolin

EntireName: 26S proteasome complexed with midnolin
Components
  • Complex: 26S proteasome complexed with midnolin
    • Complex: midnolin
      • Complex: 26S proteasome
        • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 2
      • Protein or peptide: Midnolin

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Supramolecule #1: 26S proteasome complexed with midnolin

SupramoleculeName: 26S proteasome complexed with midnolin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: midnolin

SupramoleculeName: midnolin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 26S proteasome

SupramoleculeName: 26S proteasome / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Midnolin

MacromoleculeName: Midnolin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.278652 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPQPGGARS CRRGAPGGAC ELGPAAEAAP MSLAIHSTTG TRYDLAVPPD ETVEGLRKRL SQRLKVPKER LALLHKDTRL SSGKLQEFG VGDGSKLTLV PTVEAGLMSQ ASRPEQSVMQ ALESLTETQV SDFLSGRSPL TLALRVGDHM MFVQLQLAAQ H APLQHRHV ...String:
MEPQPGGARS CRRGAPGGAC ELGPAAEAAP MSLAIHSTTG TRYDLAVPPD ETVEGLRKRL SQRLKVPKER LALLHKDTRL SSGKLQEFG VGDGSKLTLV PTVEAGLMSQ ASRPEQSVMQ ALESLTETQV SDFLSGRSPL TLALRVGDHM MFVQLQLAAQ H APLQHRHV LAAAAAAAAA RGDPSIASPV SSPCRPVSSA ARVPPVPTSP SPASPSPITA GSFRSHAAST TCPEQMDCSP TA SSSASPG ASTTSTPGAS PAPRSRKPGA VIESFVNHAP GVFSGTFSGT LHPNCQDSSG RPRRDIGTIL QILNDLLSAT RHY QGMPPS LAQLRCHAQC SPASPAPDLA PRTTSCEKLT AAPSASLLQG QSQIRMCKPP GDRLRQTENR ATRCKVERLQ LLLQ QKRLR RKARRDARGP YHWSPSRKAG RSDSSSSGGG GSPSEASGLG LDFEDSVWKP EVNPDIKSEF VVA

UniProtKB: Midnolin

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

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.313625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGGRDKAP VQPQQSPAAA PGGTDEKPSG KERRDAGDKD KEQELSEEDK QLQDELEMLV ERLGEKDTSL YRPALEELRR QIRSSTTSM TSVPKPLKFL RPHYGKLKEI YENMAPGENK RFAADIISVL AMTMSGEREC LKYRLVGSQE ELASWGHEYV R HLAGEVAK ...String:
MEEGGRDKAP VQPQQSPAAA PGGTDEKPSG KERRDAGDKD KEQELSEEDK QLQDELEMLV ERLGEKDTSL YRPALEELRR QIRSSTTSM TSVPKPLKFL RPHYGKLKEI YENMAPGENK RFAADIISVL AMTMSGEREC LKYRLVGSQE ELASWGHEYV R HLAGEVAK EWQELDDAEK VQREPLLTLV KEIVPYNMAH NAEHEACDLL MEIEQVDMLE KDIDENAYAK VCLYLTSCVN YV PEPENSA LLRCALGVFR KFSRFPEALR LALMLNDMEL VEDIFTSCKD VVVQKQMAFM LGRHGVFLEL SEDVEEYEDL TEI MSNVQL NSNFLALARE LDIMEPKVPD DIYKTHLENN RFGGSGSQVD SARMNLASSF VNGFVNAAFG QDKLLTDDGN KWLY KNKDH GMLSAAASLG MILLWDVDGG LTQIDKYLYS SEDYIKSGAL LACGIVNSGV RNECDPALAL LSDYVLHNSN TMRLG SIFG LGLAYAGSNR EDVLTLLLPV MGDSKSSMEV AGVTALACGM IAVGSCNGDV TSTILQTIME KSETELKDTY ARWLPL GLG LNHLGKGEAI EAILAALEVV SEPFRSFANT LVDVCAYAGS GNVLKVQQLL HICSEHFDSK EKEEDKDKKE KKDKDKK EA PADMGAHQGV AVLGIALIAM GEEIGAEMAL RTFGHLLRYG EPTLRRAVPL ALALISVSNP RLNILDTLSK FSHDADPE V SYNSIFAMGM VGSGTNNARL AAMLRQLAQY HAKDPNNLFM VRLAQGLTHL GKGTLTLCPY HSDRQLMSQV AVAGLLTVL VSFLDVRNII LGKSHYVLYG LVAAMQPRML VTFDEELRPL PVSVRVGQAV DVVGQAGKPK TITGFQTHTT PVLLAHGERA ELATEEFLP VTPILEGFVI LRKNPNYDL

UniProtKB: 26S proteasome non-ATPase regulatory subunit 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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