[English] 日本語
Yorodumi
- PDB-2yno: yeast betaprime COP 1-304H6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yno
Titleyeast betaprime COP 1-304H6
Components
  • COATOMER SUBUNIT BETA'
  • POLY ALA
KeywordsPROTEIN TRANSPORT / MEMBRANE TRAFFICKING / COPI-MEDIATED TRAFFICKING / DILYSINE MOTIFS
Function / homology
Function and homology information


COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intracellular mRNA localization / late endosome to vacuole transport via multivesicular body sorting pathway / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / intracellular protein transport ...COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intracellular mRNA localization / late endosome to vacuole transport via multivesicular body sorting pathway / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / intracellular protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / Coatomer WD associated region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats ...Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / Coatomer WD associated region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Coatomer subunit beta'
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
UNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsJackson, L.P. / Lewis, M. / Kent, H.M. / Edeling, M.A. / Evans, P.R. / Duden, R. / Owen, D.J.
CitationJournal: Dev.Cell / Year: 2012
Title: Molecular Basis for Recognition of Dilysine Trafficking Motifs by Copi.
Authors: Jackson, L.P. / Lewis, M. / Kent, H.M. / Edeling, M.A. / Evans, P.R. / Duden, R. / Owen, D.J.
History
DepositionOct 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COATOMER SUBUNIT BETA'
B: COATOMER SUBUNIT BETA'
P: POLY ALA


Theoretical massNumber of molelcules
Total (without water)71,3353
Polymers71,3353
Non-polymers00
Water7,260403
1
A: COATOMER SUBUNIT BETA'


Theoretical massNumber of molelcules
Total (without water)35,4811
Polymers35,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COATOMER SUBUNIT BETA'


Theoretical massNumber of molelcules
Total (without water)35,4811
Polymers35,4811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
P: POLY ALA


  • defined by author&software
  • 373 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3731
Polymers3731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.560, 50.510, 74.470
Angle α, β, γ (deg.)90.00, 103.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2050-

HOH

21B-2038-

HOH

-
Components

#1: Protein COATOMER SUBUNIT BETA' / / BETAPRIME-COP / BETA'-COAT PROTEIN / BETA'-COP


Mass: 35480.824 Da / Num. of mol.: 2 / Fragment: WD40-REPEAT DOMAIN, RESIDUES 1-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PMW172 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P41811
#2: Protein/peptide POLY ALA


Mass: 373.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: PEPTIDE MAY BE CTFKKTN, PRESENT IN CRYSTALLISATION BUT CANNOT BE ASSIGNED DEFINITIVELY
Source: (natural) UNIDENTIFIED (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 12% PEG1500

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1
DetectorDetector: CCD / Date: May 25, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49 Å / Num. obs: 55618 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 13.09 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 10.2 / % possible all: 81.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.8→49.015 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 26.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 2824 5.1 %
Rwork0.188 --
obs0.1898 55618 96.37 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.435 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.207 Å20 Å20.2424 Å2
2---3.1393 Å20 Å2
3---6.3462 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 0 403 5442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075240
X-RAY DIFFRACTIONf_angle_d1.227155
X-RAY DIFFRACTIONf_dihedral_angle_d12.4761874
X-RAY DIFFRACTIONf_chiral_restr0.088780
X-RAY DIFFRACTIONf_plane_restr0.006913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83110.25821190.19311989X-RAY DIFFRACTION75
1.8311-1.86440.25411170.19422261X-RAY DIFFRACTION82
1.8644-1.90020.2481420.19552349X-RAY DIFFRACTION88
1.9002-1.9390.231530.19822507X-RAY DIFFRACTION92
1.939-1.98120.3081240.20772613X-RAY DIFFRACTION97
1.9812-2.02730.28171420.20482725X-RAY DIFFRACTION100
2.0273-2.0780.22781300.1982761X-RAY DIFFRACTION100
2.078-2.13420.25051390.1922716X-RAY DIFFRACTION100
2.1342-2.1970.25841530.1872732X-RAY DIFFRACTION100
2.197-2.26790.25051250.19852734X-RAY DIFFRACTION100
2.2679-2.34890.23941500.19072697X-RAY DIFFRACTION100
2.3489-2.4430.20731380.18892745X-RAY DIFFRACTION100
2.443-2.55410.23871390.19562750X-RAY DIFFRACTION100
2.5541-2.68880.2161480.19462712X-RAY DIFFRACTION100
2.6888-2.85720.23681600.20732727X-RAY DIFFRACTION100
2.8572-3.07780.24561440.20992746X-RAY DIFFRACTION100
3.0778-3.38750.21811480.2022742X-RAY DIFFRACTION100
3.3875-3.87750.18191540.1742750X-RAY DIFFRACTION99
3.8775-4.88450.16721550.14712730X-RAY DIFFRACTION99
4.8845-49.03330.20071440.17052808X-RAY DIFFRACTION98

+
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