[English] 日本語
Yorodumi
- PDB-2z5e: Crystal Structure of Proteasome Assembling Chaperone 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2z5e
TitleCrystal Structure of Proteasome Assembling Chaperone 3
ComponentsProteasome Assembling Chaperone 3
KeywordsCHAPERONE / BETA SANDWICH / HOMODIMER / PROTEASOME
Function / homology
Function and homology information


Proteasome assembly / chaperone-mediated protein complex assembly / proteasome assembly / molecular adaptor activity / protein-containing complex binding / protein-containing complex / cytosol
Similarity search - Function
Ribosomal Protein S5; domain 2 - #90 / Proteasome assembly chaperone 3 / Proteasome assembly chaperone 3 / : / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome assembly chaperone 3 / Proteasome assembly chaperone 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsOkamoto, K. / Kurimoto, E. / Sakata, E. / Suzuki, A. / Yamane, T. / Hirano, Y. / Murata, S. / Tanaka, K. / Kato, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes
Authors: Yashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Niwa, S. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Takagi, K. / Suzuki, A. / Hirano, Y. / ...Authors: Yashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Niwa, S. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Takagi, K. / Suzuki, A. / Hirano, Y. / Murata, S. / Kato, K. / Yamane, T. / Tanaka, K.
History
DepositionJul 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome Assembling Chaperone 3
B: Proteasome Assembling Chaperone 3


Theoretical massNumber of molelcules
Total (without water)26,2372
Polymers26,2372
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-25.6 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.642, 88.642, 57.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Proteasome Assembling Chaperone 3 / Hypothetical protein MGC10911


Mass: 13118.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSF-Duet I / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4D216, UniProt: Q9BT73*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30%(w/v) PEG4000, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 25, 2006
RadiationMonochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→62.99 Å / Num. all: 15971 / Num. obs: 15971 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.452 / Num. unique all: 1574 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
DENZOdata reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→27.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.407 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25221 793 5 %RANDOM
Rwork0.18016 ---
all0.1836 15135 --
obs0.1836 15135 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: 26.097 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.193 Å0.209 Å
Refinement stepCycle: LAST / Resolution: 2→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 0 255 2138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221915
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9882617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52425.59359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0615358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.874156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021346
X-RAY DIFFRACTIONr_nbd_refined0.2120.2917
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.221
X-RAY DIFFRACTIONr_mcbond_it1.2021.51292
X-RAY DIFFRACTIONr_mcangle_it1.91322060
X-RAY DIFFRACTIONr_scbond_it2.7913692
X-RAY DIFFRACTIONr_scangle_it4.474.5552
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 69 -
Rwork0.189 1084 -
obs-1084 100 %

+
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