[English] 日本語
Yorodumi
- PDB-5msk: Mouse PA28beta -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5msk
TitleMouse PA28beta
ComponentsProteasome activator complex subunit 2
KeywordsSTRUCTURAL PROTEIN / heptamer / REGbeta / interferon-gamma / hydrolase
Function / homology
Function and homology information


Proteasome assembly / proteasome activator complex / antigen processing and presentation of exogenous antigen
Similarity search - Function
Proteasome activator PA28, N-terminal domain / Proteasome activator PA28, N-terminal domain superfamily / Proteasome activator PA28, N-terminal / Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal
Similarity search - Domain/homology
Proteasome activator complex subunit 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Structure / Year: 2017
Title: The Mammalian Proteasome Activator PA28 Forms an Asymmetric alpha 4 beta 3 Complex.
Authors: Huber, E.M. / Groll, M.
History
DepositionJan 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome activator complex subunit 2
B: Proteasome activator complex subunit 2
C: Proteasome activator complex subunit 2
D: Proteasome activator complex subunit 2
E: Proteasome activator complex subunit 2
F: Proteasome activator complex subunit 2
G: Proteasome activator complex subunit 2


Theoretical massNumber of molelcules
Total (without water)189,6607
Polymers189,6607
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.840, 132.610, 90.930
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A15 - 100
2112B15 - 100
3112C15 - 100
4112D15 - 100
5112E15 - 100
6112F15 - 100
7112G15 - 100
1212A108 - 190
2212B108 - 190
3212C108 - 190
4212D108 - 190
5212E108 - 190
6212F108 - 190
7212G108 - 190
1312A200 - 500
2312B200 - 500
3312C200 - 500
4312D200 - 500
5312E200 - 500
6312F200 - 500
7312G200 - 500

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.663489, 0.738775, -0.118296), (-0.746015, 0.641204, -0.179775), (-0.056961, 0.207529, 0.976569)-67.07827, 73.867, -20.75862
3given(-0.13939, 0.936202, -0.32264), (-0.953384, -0.21494, -0.2118), (-0.267636, 0.278077, 0.922521)-53.33957, 180.47942, -18.8675
4given(-0.761819, 0.427112, -0.487039), (-0.462357, -0.885109, -0.052988), (-0.453714, 0.184819, 0.871771)34.31738, 231.82544, 0.15114
5given(-0.784174, -0.426026, -0.451191), (0.392494, -0.903694, 0.171131), (-0.480644, -0.042893, 0.875866)129.86751, 194.85144, 26.87145
6given(-0.169061, -0.945353, -0.278794), (0.924152, -0.250366, 0.288549), (-0.342581, -0.208865, 0.915977)160.09685, 96.53021, 38.95714
7given(0.637425, -0.766775, -0.075799), (0.761296, 0.611577, 0.215413), (-0.118816, -0.195015, 0.973577)103.06928, 7.88283, 27.20307

-
Components

#1: Protein
Proteasome activator complex subunit 2 / 11S regulator complex subunit beta / REG-beta / Activator of multicatalytic protease subunit 2 / ...11S regulator complex subunit beta / REG-beta / Activator of multicatalytic protease subunit 2 / Proteasome activator 28 subunit beta / PA28beta


Mass: 27094.283 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psme2, Pa28b1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Solu / References: UniProt: P97372

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MgCl2, 0.1 M MES, 30 % PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→40 Å / Num. obs: 23433 / % possible obs: 97.7 % / Redundancy: 3.13 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.6
Reflection shellResolution: 3.6→3.7 Å / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSJ

5msj


Resolution: 3.6→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.926 / SU B: 98.523 / SU ML: 0.621 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26311 1170 5 %RANDOM
Rwork0.24162 ---
obs0.24269 22234 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 112.202 Å2
Baniso -1Baniso -2Baniso -3
1--7.49 Å2-0 Å2-2.19 Å2
2--6.24 Å20 Å2
3---1.41 Å2
Refinement stepCycle: 1 / Resolution: 3.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11546 0 0 0 11546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911754
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.641.98215909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.26851437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97524.518529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97152154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9181575
X-RAY DIFFRACTIONr_chiral_restr0.1290.21846
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218679
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8957.6395790
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6611.4457213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6777.6745964
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.99417647
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A714medium positional0.060.5
B714medium positional0.090.5
C714medium positional0.110.5
D714medium positional0.070.5
E714medium positional0.060.5
F714medium positional0.070.5
G714medium positional0.040.5
A716tight thermal9.990.5
B716tight thermal10.530.5
C716tight thermal4.040.5
D716tight thermal4.450.5
E716tight thermal5.310.5
F716tight thermal8.650.5
G716tight thermal9.750.5
A714medium thermal10.022
B714medium thermal10.992
C714medium thermal4.342
D714medium thermal4.642
E714medium thermal5.672
F714medium thermal9.332
G714medium thermal10.442
LS refinement shellResolution: 3.6→3.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 87 -
Rwork0.355 1649 -
obs--99.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8032-0.4212-1.15280.7099-0.85064.41570.06550.0809-0.5177-0.13780.0063-0.0290.0153-0.0569-0.07180.2392-0.0544-0.03760.23510.02020.543236.032299.7397115.1677
21.43030.0456-0.49260.1242-0.33082.1496-0.04190.0723-0.0510.02530.0677-0.13740.0929-0.1792-0.02580.3436-0.0165-0.03150.24810.04040.361641.4346120.5913116.9766
31.2651-0.02061.27470.0273-0.0843.3997-0.0042-0.00560.5613-0.03310.0588-0.02480.3991-0.2084-0.05460.2890.0175-0.03090.22320.02670.499228.3851138.674112.2568
41.89880.15830.99770.08840.28691.3142-0.19570.0830.88780.0188-0.09380.07450.1459-0.09580.28950.27050.0181-0.1040.1523-0.03120.58397.6494139.1251106.8898
51.6973-0.2281-0.17661.51441.79312.2262-0.0222-0.01970.11950.09540.06350.12780.16010.1596-0.04130.3330.02170.00760.2251-0.07770.4238-6.3675121.2052103.1348
62.5245-0.8492-0.03080.29810.07180.77610.3427-0.1458-0.5391-0.15710.08290.1638-0.20040.1216-0.42560.2402-0.1044-0.03750.1186-0.08780.5681-2.336100.5823105.628
71.6492-0.077-0.34040.1246-0.44352.32440.4633-0.0385-0.7817-0.08220.0550.1554-0.0374-0.146-0.51820.2334-0.0394-0.1470.02690.07610.760316.289490.2645111.0622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 243
2X-RAY DIFFRACTION2B3 - 245
3X-RAY DIFFRACTION3C9 - 245
4X-RAY DIFFRACTION4D3 - 241
5X-RAY DIFFRACTION5E11 - 242
6X-RAY DIFFRACTION6F5 - 243
7X-RAY DIFFRACTION7G4 - 243

+
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