[English] 日本語
Yorodumi
- EMDB-8662: Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Chann... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8662
TitleNucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated Human 26S Proteasome
Map dataFinal map corrected with a B-factor of -80
Sample
  • Complex: 26S proteasome bound to ATP-gammaS
    • Protein or peptide: x 14 types
Keywords26S proteasome / ATP-dependent protease / AAA-ATPase / peptide-unfolding channel / 20S core particle / HYDROLASE
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of inflammatory response to antigenic stimulus / Degradation of AXIN / P-body / Hh mutants are degraded by ERAD / lipopolysaccharide binding / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G2/M Checkpoints / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Regulation of RUNX3 expression and activity / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / 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 / response to virus / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / nuclear matrix / 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 / peptidase activity / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / regulation of inflammatory response / response to oxidative stress / secretory granule lumen / endopeptidase activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / nuclear body / cilium / ciliary basal body / ribosome / cadherin binding / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / mitochondrion / proteolysis / RNA binding / extracellular exosome / extracellular region
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit ...Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 ...Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhu Y / Wang WL
CitationJournal: Nat Commun / Year: 2018
Title: Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Authors: Yanan Zhu / Wei Li Wang / Daqi Yu / Qi Ouyang / Ying Lu / Youdong Mao /
Abstract: The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase ...The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all known eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of the substrate-translocation channel leading to the proteolytic chamber of the core particle (CP). Here we report three alternative states of the ATP-γ-S-bound human proteasome, in which the CP gates are asymmetrically open, visualized by cryo-EM at near-atomic resolutions. At least four nucleotides are bound to the AAA-ATPase ring in these open-gate states. Variation in nucleotide binding gives rise to an axial movement of the pore loops narrowing the substrate-translation channel, which exhibit remarkable structural transitions between the spiral-staircase and saddle-shaped-circle topologies. Gate opening in the CP is thus regulated by nucleotide-driven conformational changes of the AAA-ATPase unfoldase. These findings demonstrate an elegant mechanism of allosteric coordination among sub-machines within the human proteasome holoenzyme.
History
DepositionApr 8, 2017-
Header (metadata) releaseSep 20, 2017-
Map releaseJul 18, 2018-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5vfo
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8662.png

Downloads & links

-
Map

FileDownload / File: emd_8662.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map corrected with a B-factor of -80
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 560 pix.
= 420. Å		0.75 Å/pix.
x 560 pix.
= 420. Å		0.75 Å/pix.
x 560 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.012748035 - 0.02731222
Average (Standard dev.)0.000030307066 (±0.001778131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.750.750.75
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0130.0270.000

-
Supplemental data

-
Additional map: Uncorrected raw map

Fileemd_8662_additional.map
AnnotationUncorrected raw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : 26S proteasome bound to ATP-gammaS

EntireName: 26S proteasome bound to ATP-gammaS
Components
  • Complex: 26S proteasome bound to ATP-gammaS
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Proteasome subunit alpha type-7
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta type-7
    • Protein or peptide: Proteasome subunit beta type-3
    • Protein or peptide: Proteasome subunit beta type-2
    • Protein or peptide: Proteasome subunit beta type-5
    • Protein or peptide: Proteasome subunit beta type-1
    • Protein or peptide: Proteasome subunit beta type-4

+
Supramolecule #1: 26S proteasome bound to ATP-gammaS

SupramoleculeName: 26S proteasome bound to ATP-gammaS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.727658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSAGFDRHIT IFSPEGRLYQ VEYAFKAINQ GGLTSVAVRG KDCAVIVTQK KVPDKLLDSS TVTHLFKITE NIGCVMTGMT ADSRSQVQR ARYEAANWKY KYGYEIPVDM LCKRIADISQ VYTQNAEMRP LGCCMILIGI DEEQGPQVYK CDPAGYYCGF K ATAAGVKQ ...String:
SSAGFDRHIT IFSPEGRLYQ VEYAFKAINQ GGLTSVAVRG KDCAVIVTQK KVPDKLLDSS TVTHLFKITE NIGCVMTGMT ADSRSQVQR ARYEAANWKY KYGYEIPVDM LCKRIADISQ VYTQNAEMRP LGCCMILIGI DEEQGPQVYK CDPAGYYCGF K ATAAGVKQ TESTSFLEKK VKKKFDWTFE QTVETAITCL STVLSIDFKP SEIEVGVVTV ENPKFRILTE AEIDAHLVAL AE

UniProtKB: Proteasome subunit alpha type-6

+
Macromolecule #2: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.72526 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ERGYSFSLTT FSPSGKLVQI EYALAAVAGG APSVGIKAAN GVVLATEKKQ KSILYDERSV HKVEPITKHI GLVYSGMGPD YRVLVHRAR KLAQQYYLVY QEPIPTAQLV QRVASVMQEY TQSGGVRPFG VSLLICGWNE GRPYLFQSDP SGAYFAWKAT A MGKNYVNG ...String:
ERGYSFSLTT FSPSGKLVQI EYALAAVAGG APSVGIKAAN GVVLATEKKQ KSILYDERSV HKVEPITKHI GLVYSGMGPD YRVLVHRAR KLAQQYYLVY QEPIPTAQLV QRVASVMQEY TQSGGVRPFG VSLLICGWNE GRPYLFQSDP SGAYFAWKAT A MGKNYVNG KTFLEKRYNE DLELEDAIHT AILTLKESFE GQMTEDNIEV GICNEAGFRR LTPTEVKDYL AAIA

UniProtKB: Proteasome subunit alpha type-2

+
Macromolecule #3: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.118189 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SRRYDSRTTI FSPEGRLYQV EYAMEAIGHA GTCLGILAND GVLLAAERRN IHKLLDEVFF SEKIYKLNED MACSVAGITS DANVLTNEL RLIAQRYLLQ YQEPIPCEQL VTALCDIKQA YTQFGGKRPF GVSLLYIGWD KHYGFQLYQS DPSGNYGGWK A TCIGNNSA ...String:
SRRYDSRTTI FSPEGRLYQV EYAMEAIGHA GTCLGILAND GVLLAAERRN IHKLLDEVFF SEKIYKLNED MACSVAGITS DANVLTNEL RLIAQRYLLQ YQEPIPCEQL VTALCDIKQA YTQFGGKRPF GVSLLYIGWD KHYGFQLYQS DPSGNYGGWK A TCIGNNSA AAVSMLKQDY KEGEMTLKSA LALAIKVLNK TMDVSKLSAE KVEIATLTRE NGKTVIRVLK QKEVEQLIKK HE EEEAKAE REK

UniProtKB: Proteasome subunit alpha type-4

+
Macromolecule #4: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.382178 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYDRAITVFS PDGHLFQVEY AQEAVKKGST AVGVRGRDIV VLGVEKKSVA KLQDERTVRK ICALDDNVCM AFAGLTADAR IVINRARVE CQSHRLTVED PVTVEYITRY IASLKQRYTQ SNGRRPFGIS ALIVGFDFDG TPRLYQTDPS GTYHAWKANA I GRGAKSVR ...String:
SYDRAITVFS PDGHLFQVEY AQEAVKKGST AVGVRGRDIV VLGVEKKSVA KLQDERTVRK ICALDDNVCM AFAGLTADAR IVINRARVE CQSHRLTVED PVTVEYITRY IASLKQRYTQ SNGRRPFGIS ALIVGFDFDG TPRLYQTDPS GTYHAWKANA I GRGAKSVR EFLEKNYTDE AIETDDLTIK LVIKALLEVV QSGGKNIELA VMRRDQSLKI LNPEEIEKYV AEIEKEKEEN EK KKQ

UniProtKB: Proteasome subunit alpha type-7

+
Macromolecule #5: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.569957 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YDRGVNTFSP EGRLFQVEYA IEAIKLGSTA IGIQTSEGVC LAVEKRITSP LMEPSSIEKI VEIDAHIGCA MSGLIADAKT LIDKARVET QNHWFTYNET MTVESVTQAV SNLALQFGEE DADPGAMSRP FGVALLFGGV DEKGPQLFHM DPSGTFVQCD A RAIGSASE ...String:
YDRGVNTFSP EGRLFQVEYA IEAIKLGSTA IGIQTSEGVC LAVEKRITSP LMEPSSIEKI VEIDAHIGCA MSGLIADAKT LIDKARVET QNHWFTYNET MTVESVTQAV SNLALQFGEE DADPGAMSRP FGVALLFGGV DEKGPQLFHM DPSGTFVQCD A RAIGSASE GAQSSLQEVY HKSMTLKEAI KSSLIILKQV MEEKLNATNI ELATVQPGQN FHMFTKEELE EVIKDI

UniProtKB: Proteasome subunit alpha type-5

+
Macromolecule #6: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.728428 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NQYDNDVTVW SPQGRIHQIE YAMEAVKQGS ATVGLKSKTH AVLVALKRAQ SELAAHQKKI LHVDNHIGIS IAGLTADARL LCNFMRQEC LDSRFVFDRP LPVSRLVSLI GSKTQIPTQR YGRRPYGVGL LIAGYDDMGP HIFQTCPSAN YFDCRAMSIG A RSQSARTY ...String:
NQYDNDVTVW SPQGRIHQIE YAMEAVKQGS ATVGLKSKTH AVLVALKRAQ SELAAHQKKI LHVDNHIGIS IAGLTADARL LCNFMRQEC LDSRFVFDRP LPVSRLVSLI GSKTQIPTQR YGRRPYGVGL LIAGYDDMGP HIFQTCPSAN YFDCRAMSIG A RSQSARTY LERHMSEFME CNLNELVKHG LRALRETLPA EQDLTTKNVS IGIVGKDLEF TIYDDDDVSP FLEGLEERPQ

UniProtKB: Proteasome subunit alpha type-1

+
Macromolecule #7: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.2871 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SSIGTGYDLS ASTFSPDGRV FQVEYAMKAV ENSSTAIGIR CKDGVVFGVE KLVLSKLYEE GSNKRLFNVD RHVGMAVAGL LADARSLAD IAREEASNFR SNFGYNIPLK HLADRVAMYV HAYTLYSAVR PFGCSFMLGS YSVNDGAQLY MIDPSGVSYG Y WGCAIGKA ...String:
SSIGTGYDLS ASTFSPDGRV FQVEYAMKAV ENSSTAIGIR CKDGVVFGVE KLVLSKLYEE GSNKRLFNVD RHVGMAVAGL LADARSLAD IAREEASNFR SNFGYNIPLK HLADRVAMYV HAYTLYSAVR PFGCSFMLGS YSVNDGAQLY MIDPSGVSYG Y WGCAIGKA RQAAKTEIEK LQMKEMTCRD IVKEVAKIIY IVHDEVKDKA FELELSWVGE LTNGRHEIVP KDIREEAEKY AK ESLKE

UniProtKB: Proteasome subunit alpha type-3

+
Macromolecule #8: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.471129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TTIMAVQFDG GVVLGADSRT TTGSYIANRV TDKLTPIHDR IFCCRSGSAA DTQAVADAVT YQLGFHSIEL NEPPLVHTAA SLFKEMCYR YREDLMAGII IAGWDPQEGG QVYSVPMGGM MVRQSFAIGG SGSSYIYGYV DATYREGMTK EECLQFTANA L ALAMERDG SSGGVIRLAA IAESGVERQV LLG

UniProtKB: Proteasome subunit beta type-6

+
Macromolecule #9: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.745256 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTIAGVVYKD GIVLGADTRA TEGMVVADKN CSKIHFISPN IYCCGAGTAA DTDMTTQLIS SNLELHSLST GRLPRVVTAN RMLKQMLFR YQGYIGAALV LGGVDVTGPH LYSIYPHGST DKLPYVTMGS GSLAAMAVFE DKFRPDMEEE EAKNLVSEAI A AGIFNDLG ...String:
TTIAGVVYKD GIVLGADTRA TEGMVVADKN CSKIHFISPN IYCCGAGTAA DTDMTTQLIS SNLELHSLST GRLPRVVTAN RMLKQMLFR YQGYIGAALV LGGVDVTGPH LYSIYPHGST DKLPYVTMGS GSLAAMAVFE DKFRPDMEEE EAKNLVSEAI A AGIFNDLG SGSNIDLCVI SKNKLDFLRP YTVPNKKGTR LGRYRCEKGT TAVLTEKITP LE

UniProtKB: Proteasome subunit beta type-7

+
Macromolecule #10: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.841701 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIMSYNGGAV MAMKGKNCVA IAADRRFGIQ AQMVTTDFQK IFPMGDRLYI GLAGLATDVQ TVAQRLKFRL NLYELKEGRQ IKPYTLMSM VANLLYEKRF GPYYTEPVIA GLDPKTFKPF ICSLDLIGCP MVTDDFVVSG TCAEQMYGMC ESLWEPNMDP D HLFETISQ ...String:
SIMSYNGGAV MAMKGKNCVA IAADRRFGIQ AQMVTTDFQK IFPMGDRLYI GLAGLATDVQ TVAQRLKFRL NLYELKEGRQ IKPYTLMSM VANLLYEKRF GPYYTEPVIA GLDPKTFKPF ICSLDLIGCP MVTDDFVVSG TCAEQMYGMC ESLWEPNMDP D HLFETISQ AMLNAVDRDA VSGMGVIVHI IEKDKITTRT LKARMD

UniProtKB: Proteasome subunit beta type-3

+
Macromolecule #11: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.720146 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ ...String:
MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ KRFILNLPTF SVRIIDKNGI HDLDNISFPK Q

UniProtKB: Proteasome subunit beta type-2

+
Macromolecule #12: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.199072 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTTLAFKFRH GVIVAADSRA TAGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQ YKGMGLSMGT MICGWDKRGP GLYYVDSEGN RISGATFSVG SGSVYAYGVM DRGYSYDLEV EQAYDLARRA I YQATYRDA ...String:
TTTLAFKFRH GVIVAADSRA TAGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQ YKGMGLSMGT MICGWDKRGP GLYYVDSEGN RISGATFSVG SGSVYAYGVM DRGYSYDLEV EQAYDLARRA I YQATYRDA YSGGAVNLYH VREDGWIRVS SDNVADLHEK YSG

UniProtKB: Proteasome subunit beta type-5

+
Macromolecule #13: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.578986 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RFSPYVFNGG TILAIAGEDF AIVASDTRLS EGFSIHTRDS PKCYKLTDKT VIGCSGFHGD CLTLTKIIEA RLKMYKHSNN KAMTTGAIA AMLSTILYSR RFFPYYVYNI IGGLDEEGKG AVYSFDPVGS YQRDSFKAGG SASAMLQPLL DNQVGFKNMQ N VEHVPLSL ...String:
RFSPYVFNGG TILAIAGEDF AIVASDTRLS EGFSIHTRDS PKCYKLTDKT VIGCSGFHGD CLTLTKIIEA RLKMYKHSNN KAMTTGAIA AMLSTILYSR RFFPYYVYNI IGGLDEEGKG AVYSFDPVGS YQRDSFKAGG SASAMLQPLL DNQVGFKNMQ N VEHVPLSL DRAMRLVKDV FISAAERDVY TGDALRICIV TKEGIREETV SLRKD

UniProtKB: Proteasome subunit beta type-1

+
Macromolecule #14: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.994324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TQNPMVTGTS VLGVKFEGGV VIAADMLGSY GSLARFRNIS RIMRVNNSTM LGASGDYADF QYLKQVLGQM VIDEELLGDG HSYSPRAIH SWLTRAMYSR RSKMNPLWNT MVIGGYADGE SFLGYVDMLG VAYEAPSLAT GYGAYLAQPL LREVLEKQPV L SQTEARDL ...String:
TQNPMVTGTS VLGVKFEGGV VIAADMLGSY GSLARFRNIS RIMRVNNSTM LGASGDYADF QYLKQVLGQM VIDEELLGDG HSYSPRAIH SWLTRAMYSR RSKMNPLWNT MVIGGYADGE SFLGYVDMLG VAYEAPSLAT GYGAYLAQPL LREVLEKQPV L SQTEARDL VERCMRVLYY RDARSYNRFQ IATVTEKGVE IEGPLSTETN WDIAHMI

UniProtKB: Proteasome subunit beta type-4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228086
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more