[English] 日本語
Yorodumi
- PDB-4j73: Crystal structure of beta'-COP/p25 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j73
TitleCrystal structure of beta'-COP/p25 complex
Components
  • Coatomer subunit beta'
  • Transmembrane emp24 domain-containing protein 9
KeywordsPROTEIN TRANSPORT / beta propeller / dilysine motif / ER retrieval signal / coatomer cargo recognition
Function / homology
Function and homology information


COPI coating of Golgi vesicle / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / positive regulation of organelle organization / 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 ...COPI coating of Golgi vesicle / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / positive regulation of organelle organization / 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 / syntaxin binding / COPII-coated ER to Golgi transport vesicle / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / ubiquitin binding / intracellular protein transport / synaptic vesicle / membrane => GO:0016020 / Golgi membrane / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
emp24/gp25L/p24 family/GOLD / emp24/gp25L/p24 family/GOLD / Transmembrane emp24 domain-containing protein / GOLD domain / GOLD domain profile. / Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / Coatomer WD associated region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller ...emp24/gp25L/p24 family/GOLD / emp24/gp25L/p24 family/GOLD / Transmembrane emp24 domain-containing protein / GOLD domain / GOLD domain profile. / 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' / Transmembrane emp24 domain-containing protein 9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.439 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Embo J. / Year: 2013
Title: Rules for the recognition of dilysine retrieval motifs by coatomer.
Authors: Ma, W. / Goldberg, J.
History
DepositionFeb 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Coatomer subunit beta'
B: Transmembrane emp24 domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)35,1302
Polymers35,1302
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint2 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.295, 56.696, 132.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Coatomer subunit beta' / / Beta'-coat protein / Beta'-COP


Mass: 34293.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41811
#2: Protein/peptide Transmembrane emp24 domain-containing protein 9 / p25 / p24 family protein alpha-2 / p24alpha2


Mass: 836.029 Da / Num. of mol.: 1 / Fragment: UNP residues 229-236 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: Q3T133
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.54 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.439→66.176 Å / Num. all: 48875 / Num. obs: 48785 / % possible obs: 96.8 % / Observed criterion σ(I): 15.6

-
Processing

Software
NameVersionClassification
ADSCdata collection
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.439→31.823 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1997 4.09 %RANDOM
Rwork0.1774 ---
obs0.1783 48785 96.47 %-
all-48875 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.439→31.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 0 301 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112453
X-RAY DIFFRACTIONf_angle_d1.4713347
X-RAY DIFFRACTIONf_dihedral_angle_d13.334855
X-RAY DIFFRACTIONf_chiral_restr0.1375
X-RAY DIFFRACTIONf_plane_restr0.009421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.439-1.47460.26661060.28892479X-RAY DIFFRACTION74
1.4746-1.51440.27471320.26613130X-RAY DIFFRACTION91
1.5144-1.5590.27641430.24783345X-RAY DIFFRACTION99
1.559-1.60930.23611440.22473377X-RAY DIFFRACTION99
1.6093-1.66680.22911450.19963389X-RAY DIFFRACTION99
1.6668-1.73350.25251450.18823403X-RAY DIFFRACTION99
1.7335-1.81240.20661460.1823414X-RAY DIFFRACTION99
1.8124-1.9080.19891440.17063401X-RAY DIFFRACTION99
1.908-2.02750.2011470.15783423X-RAY DIFFRACTION99
2.0275-2.1840.19421460.15753419X-RAY DIFFRACTION99
2.184-2.40370.20471480.16733455X-RAY DIFFRACTION99
2.4037-2.75140.18161480.17933460X-RAY DIFFRACTION100
2.7514-3.46580.19461500.1663520X-RAY DIFFRACTION100
3.4658-31.83070.1821530.17063573X-RAY DIFFRACTION96
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)
10.3472-0.0722-0.23350.4857-0.2610.3312-0.02420.4490.2044-0.12120.09030.1165-0.0349-0.0271-00.26860.0004-0.00820.43960.09560.241610.37025.6467-28.4473
21.5512-0.0879-0.5090.4618-0.291.1469-0.03130.2494-0.1553-0.0376-0.0120.04280.15740.1120.00010.21220.0277-0.00260.2157-0.01880.2087.4349-11.1181-16.1102
30.97220.3085-0.14350.5662-0.14810.78710.02460.11360.2090.0680.02520.0932-0.20540.08140.00010.24720.00620.00880.18440.03630.26115.49627.9359-10.1995
40.0082-0.0070.00170.0159-0.01160.01-0.31820.0375-0.0028-0.0859-0.25220.2026-0.2424-0.02760.00010.26170.0272-0.04360.3607-0.01470.3269-10.2414-4.1628-18.804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 301 )
4X-RAY DIFFRACTION4chain 'B' and (resid -3 through 2 )

+
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