[English] 日本語
Yorodumi
- PDB-1z7q: Crystal structure of the 20s proteasome from yeast in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z7q
TitleCrystal structure of the 20s proteasome from yeast in complex with the proteasome activator PA26 from Trypanosome brucei at 3.2 angstroms resolution
Components
  • (Proteasome component ...) x 13
  • Potential proteasome component C5
  • proteasome activator protein PA26
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / 20S / proteasome / PA26 / activator / multi-catalytic protease / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


proteasome activator complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 ...proteasome activator complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / endopeptidase activator activity / Ub-specific processing proteases / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / proteolysis / nucleus / cytosol
Similarity search - Function
Proteasome activator pa28, C-terminal domain / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 ...Proteasome activator pa28, C-terminal domain / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 4-Layer Sandwich / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome activator protein PA26
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Trypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsForster, A. / Whitby, F.G. / Hill, C.P.
CitationJournal: Mol.Cell / Year: 2005
Title: The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions.
Authors: Forster, A. / Masters, E.I. / Whitby, F.G. / Robinson, H. / Hill, C.P.
History
DepositionMar 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 3, 2014Group: Other
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE Residue (i GLY 1172) and Residue (i GLY 1173) are not linked. Distance of C-N bond is 1.91. ...SEQUENCE Residue (i GLY 1172) and Residue (i GLY 1173) are not linked. Distance of C-N bond is 1.91. Residue (p GLY 1172) and Residue (p GLY 1173) are not linked. Distance of C-N bond is 1.91.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome component C7-alpha
B: Proteasome component Y7
C: Proteasome component Y13
D: Proteasome component PRE6
E: Proteasome component PUP2
F: Proteasome component PRE5
G: Proteasome component C1
H: Proteasome component PRE3
I: Proteasome component PUP1
J: Proteasome component PUP3
K: Proteasome component C11
L: Proteasome component PRE2
M: Potential proteasome component C5
N: Proteasome component PRE4
O: Proteasome component C7-alpha
P: Proteasome component Y7
Q: Proteasome component Y13
R: Proteasome component PRE6
S: Proteasome component PUP2
T: Proteasome component PRE5
U: Proteasome component C1
V: Proteasome component PRE3
W: Proteasome component PUP1
X: Proteasome component PUP3
Y: Proteasome component C11
Z: Proteasome component PRE2
a: Potential proteasome component C5
b: Proteasome component PRE4
c: proteasome activator protein PA26
d: proteasome activator protein PA26
e: proteasome activator protein PA26
f: proteasome activator protein PA26
g: proteasome activator protein PA26
h: proteasome activator protein PA26
i: proteasome activator protein PA26
j: proteasome activator protein PA26
k: proteasome activator protein PA26
l: proteasome activator protein PA26
m: proteasome activator protein PA26
n: proteasome activator protein PA26
o: proteasome activator protein PA26
p: proteasome activator protein PA26


Theoretical massNumber of molelcules
Total (without water)1,079,54442
Polymers1,079,54442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.964, 232.127, 296.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details1 complete, 28-subunit 20S proteasome is found in the asymmetric unit / 2 complete, 7-subunit PA26 compllexes are found in the asymmetric unit

-
Components

-
Proteasome component ... , 13 types, 26 molecules AOBPCQDRESFTGUHVIWJXKYLZNb

#1: Protein Proteasome component C7-alpha / Macropain subunit C7- alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / ...Macropain subunit C7- alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / Component Y8 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21243, proteasome endopeptidase complex
#2: Protein Proteasome component Y7 / Macropain subunit Y7 / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex subunit Y7


Mass: 27191.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#3: Protein Proteasome component Y13 / Macropain subunit Y13 / Proteinase YSCE subunit 13 / Multicatalytic endopeptidase complex subunit Y13


Mass: 28748.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#4: Protein Proteasome component PRE6 / Macropain subunit PRE6 / Proteinase YSCE subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#5: Protein Proteasome component PUP2 / Macropain subunit PUP2 / Proteinase YSCE subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#6: Protein Proteasome component PRE5 / Macropain subunit PRE5 / Proteinase YSCE subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein Proteasome component C1 / Macropain subunit C1 / Proteinase YSCE subunit 1 / Multicatalytic endopeptidase complex subunit C1


Mass: 31575.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21242, proteasome endopeptidase complex
#8: Protein Proteasome component PRE3 / Macropain subunit PRE3 / Proteinase YSCE subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex
#9: Protein Proteasome component PUP1 / Macropain subunit PUP1 / Proteinase YSCE subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1


Mass: 23987.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#10: Protein Proteasome component PUP3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22627.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#11: Protein Proteasome component C11 / Macropain subunit C11 / Proteinase YSCE subunit 11 / Multicatalytic endopeptidase complex subunit C11


Mass: 22545.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#12: Protein Proteasome component PRE2 / Macropain subunit PRE2 / Proteinase YSCE subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2


Mass: 23353.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#14: Protein Proteasome component PRE4 / Macropain subunit PRE4 / Proteinase YSCE subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30657, proteasome endopeptidase complex

-
Protein , 2 types, 16 molecules Macdefghijklmnop

#13: Protein Potential proteasome component C5 / Multicatalytic endopeptidase complex subunit C5


Mass: 24883.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#15: Protein
proteasome activator protein PA26


Mass: 25228.734 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U8G2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaHEPES, 40% MPD, 0.2 M NACL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationMonochromator: SSRL beamline 9-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 189615 / Num. obs: 189615 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.331 / % possible all: 0.0629

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: one-half of the yeast 20S proteasome (Huber, et al., high-resolution structure), pdb entry 1RYP

1ryp


Resolution: 3.22→39.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1264 -random
Rwork0.263 ---
obs0.263 189495 89.1 %-
all-189615 --
Refinement stepCycle: LAST / Resolution: 3.22→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms74222 0 0 0 74222

+
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