[English] 日本語
Yorodumi
- PDB-1q5q: The Rhodococcus 20S proteasome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q5q
TitleThe Rhodococcus 20S proteasome
Components
  • proteasome alpha-type subunit 1
  • proteasome beta-type subunit 1
KeywordsHYDROLASE / proteasome assembly / pro-peptide / inter-subunit contacts / Rhodococcus erythropolis
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 / modification-dependent protein catabolic process / endopeptidase activity / cytoplasm / cytosol
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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
Proteasome subunit beta 1 / Proteasome subunit alpha 1
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKwon, Y.D. / Nagy, I. / Adams, P.D. / Baumeister, W. / Jap, B.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly.
Authors: Kwon, Y.D. / Nagy, I. / Adams, P.D. / Baumeister, W. / Jap, B.K.
History
DepositionAug 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: proteasome alpha-type subunit 1
B: proteasome alpha-type subunit 1
C: proteasome alpha-type subunit 1
D: proteasome alpha-type subunit 1
E: proteasome alpha-type subunit 1
F: proteasome alpha-type subunit 1
G: proteasome alpha-type subunit 1
H: proteasome beta-type subunit 1
I: proteasome beta-type subunit 1
J: proteasome beta-type subunit 1
K: proteasome beta-type subunit 1
L: proteasome beta-type subunit 1
M: proteasome beta-type subunit 1
N: proteasome beta-type subunit 1


Theoretical massNumber of molelcules
Total (without water)373,32114
Polymers373,32114
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: proteasome alpha-type subunit 1
B: proteasome alpha-type subunit 1
C: proteasome alpha-type subunit 1
D: proteasome alpha-type subunit 1
E: proteasome alpha-type subunit 1
F: proteasome alpha-type subunit 1
G: proteasome alpha-type subunit 1
H: proteasome beta-type subunit 1
I: proteasome beta-type subunit 1
J: proteasome beta-type subunit 1
K: proteasome beta-type subunit 1
L: proteasome beta-type subunit 1
M: proteasome beta-type subunit 1
N: proteasome beta-type subunit 1

A: proteasome alpha-type subunit 1
B: proteasome alpha-type subunit 1
C: proteasome alpha-type subunit 1
D: proteasome alpha-type subunit 1
E: proteasome alpha-type subunit 1
F: proteasome alpha-type subunit 1
G: proteasome alpha-type subunit 1
H: proteasome beta-type subunit 1
I: proteasome beta-type subunit 1
J: proteasome beta-type subunit 1
K: proteasome beta-type subunit 1
L: proteasome beta-type subunit 1
M: proteasome beta-type subunit 1
N: proteasome beta-type subunit 1


Theoretical massNumber of molelcules
Total (without water)746,64228
Polymers746,64228
Non-polymers00
Water50428
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Buried area75580 Å2
ΔGint-35 kcal/mol
Surface area231590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)150.112, 215.307, 251.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
proteasome alpha-type subunit 1


Mass: 28346.840 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: BL21 / Gene: PRCA(1) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53080, proteasome endopeptidase complex
#2: Protein
proteasome beta-type subunit 1


Mass: 24984.766 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: BL21 / Gene: PRCB(1) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53079
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 14% PEG 6000, 50mM sodium citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
210 mMTris-HCl1droppH7.0
314 %(w/v)PEG60001reservoir
450 mMsodium citrate1reservoirpH5.4

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 114039 / Observed criterion σ(I): 0 / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.074
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 91.7 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PMA

1pma


Resolution: 2.6→19.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 183405.38 / Data cutoff high rms absF: 183405.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 11414 10 %RANDOM
Rwork0.246 ---
obs0.246 113989 91.7 %-
all-124455 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.7308 Å2 / ksol: 0.312508 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å20 Å20 Å2
2--2.48 Å20 Å2
3----7.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23539 0 0 167 23706
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.882.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 1499 9.8 %
Rwork0.319 13768 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. reflection obs: 113987
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

+
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