[English] 日本語
Yorodumi
- PDB-1j2q: 20S proteasome in complex with calpain-Inhibitor I from archaeogl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j2q
Title20S proteasome in complex with calpain-Inhibitor I from archaeoglobus fulgidus
Components
  • Proteasome alpha subunit
  • Proteasome beta subunit
KeywordsHYDROLASE / proteasome / ubiquitin / 20S / CP
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / ubiquitin-dependent protein catabolic process / cytoplasm / cytosol
Similarity search - Function
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 ...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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CIB / Proteasome subunit alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsGroll, M. / Brandstetter, H. / Bartunik, H. / Bourenkow, G. / Huber, R.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Investigations on the Maturation and Regulation of Archaebacterial Proteasomes
Authors: Groll, M. / Brandstetter, H. / Bartunik, H. / Bourenkow, G. / Huber, R.
History
DepositionJan 8, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,54121
Polymers340,85714
Non-polymers2,6857
Water1,892105
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)687,08342
Polymers681,71328
Non-polymers5,36914
Water50428
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area109540 Å2
ΔGint-262 kcal/mol
Surface area215580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)148.097, 148.097, 303.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second part of the bioogical assembly is generated by the two-fold axis: x, -y, -z+2/3

-
Components

#1: Protein
Proteasome alpha subunit


Mass: 26561.521 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: prset6c / Production host: Escherichia coli (E. coli)
References: UniProt: O29760, proteasome endopeptidase complex
#2: Protein
Proteasome beta subunit


Mass: 22132.283 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: prset6c / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P996, proteasome endopeptidase complex
#3: Chemical
ChemComp-CIB / 2-ACETYLAMINO-4-METHYL-PENTANOIC ACID [1-(1-FORMYL-PENTYLCARBAMOYL)-3-METHYL-BUTYL]-AMIDE / CALPAIN IHIBITOR I


Mass: 383.525 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C20H37N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 9% PEG 400, 80mM MgCl2, 100mM NaAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 24 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
2100 mM1reservoirpH4.6NaOAc
39 %(w/v)PEG4001reservoir
480 mM1reservoirMgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 87322 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 46.1 Å2
Reflection shellResolution: 2.83→2.88 Å / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 1140521 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Rmerge(I) obs: 0.399

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→16.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3321738.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 4404 5.1 %RANDOM
Rwork0.241 ---
all0.243 87104 --
obs0.243 87104 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.0264 Å2 / ksol: 0.307215 e/Å3
Displacement parametersBiso mean: 51.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å21.35 Å20 Å2
2---3.8 Å20 Å2
3---7.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.83→16.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23933 0 189 105 24227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.83→2.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 609 5 %
Rwork0.383 11521 -
obs--77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CAL.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

+
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://pdbjlvh1.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