[English] 日本語
Yorodumi
- PDB-1ya7: Implications for interactions of proteasome with PAN and PA700 fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ya7
TitleImplications for interactions of proteasome with PAN and PA700 from the 1.9 A structure of a proteasome-11S activator complex
Components
  • Proteasome alpha subunit
  • Proteasome beta subunit
  • proteasome activator protein PA26
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / archaeal proteasome / PA26 / copmlex / open gate / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis / cytoplasm
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 / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta-type subunits signature. ...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 / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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
: / Proteasome subunit alpha / Proteasome subunit beta / Proteasome activator protein PA26
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
Trypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsForster, A. / Masters, E.I. / Whitby, F.G. / Robinson, H. / 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
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
O: proteasome activator protein PA26
P: proteasome activator protein PA26
Q: proteasome activator protein PA26
R: proteasome activator protein PA26
S: proteasome activator protein PA26
T: proteasome activator protein PA26
U: proteasome activator protein PA26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)534,07249
Polymers531,41021
Non-polymers2,66228
Water29,8871659
1
A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
O: proteasome activator protein PA26
P: proteasome activator protein PA26
Q: proteasome activator protein PA26
R: proteasome activator protein PA26
S: proteasome activator protein PA26
T: proteasome activator protein PA26
U: proteasome activator protein PA26
hetero molecules

A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
O: proteasome activator protein PA26
P: proteasome activator protein PA26
Q: proteasome activator protein PA26
R: proteasome activator protein PA26
S: proteasome activator protein PA26
T: proteasome activator protein PA26
U: proteasome activator protein PA26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,068,14598
Polymers1,062,82142
Non-polymers5,32456
Water75742
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area194900 Å2
ΔGint-1275 kcal/mol
Surface area306750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)255.714, 126.961, 181.494
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11J-3061-

HOH

DetailsOne half of the 20S:PA26 complex forms the asymmetric unit. A crystallographic 2-fold operator runs parallel to the 2-fold symmetry axis of the full protein complex.

-
Components

-
Protein , 3 types, 21 molecules ABCDEFGHIJKLMNOPQRSTU

#1: Protein
Proteasome alpha subunit / Multicatalytic endopeptidase complex alpha subunit


Mass: 25829.447 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA / Plasmid: PRSET5A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P25156, proteasome endopeptidase complex
#2: Protein
Proteasome beta subunit / Multicatalytic endopeptidase complex beta subunit


Mass: 23998.691 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmB / Plasmid: PRSET5A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28061, proteasome endopeptidase complex
#3: Protein
proteasome activator protein PA26


Mass: 26087.643 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: PBTPA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 5757773, UniProt: Q9U8G2*PLUS

-
Non-polymers , 3 types, 1687 molecules

#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1659 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 1000, sodium phosphate citrate, LiSO4, imidazole, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.283 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 257676 / Num. obs: 257676 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.3 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1pma

1pma


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.972 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.252 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22403 991 0.4 %RANDOM
Rwork0.17961 ---
all0.17979 257676 --
obs0.17979 249402 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.254 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35035 0 147 1659 36841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02236019
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9748708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53154584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75524.3451535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.626156585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0115252
X-RAY DIFFRACTIONr_chiral_restr0.0970.25650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0226590
X-RAY DIFFRACTIONr_nbd_refined0.2140.217336
X-RAY DIFFRACTIONr_nbtor_refined0.30.225077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.22212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.2190
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.239
X-RAY DIFFRACTIONr_mcbond_it0.9731.523508
X-RAY DIFFRACTIONr_mcangle_it1.601236550
X-RAY DIFFRACTIONr_scbond_it2.482314221
X-RAY DIFFRACTIONr_scangle_it3.9364.512158
LS refinement shellResolution: 2.3→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 61 -
Rwork0.226 17323 -
obs--99.98 %

+
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