[English] 日本語
Yorodumi
- PDB-5jqp: Crystal structure of ER glucosidase II heterodimeric complex cons... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jqp
TitleCrystal structure of ER glucosidase II heterodimeric complex consisting of catalytic subunit and the binding domain of regulatory subunit
Components
  • Alpha glucosidase-like protein
  • Glucosidase 2 subunit beta-like proteinGlucosidases
KeywordsHYDROLASE / PROTEIN TRANSPORT
Function / homology
Function and homology information


alpha-glucosidase / N-glycan processing / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / endoplasmic reticulum / metal ion binding
Similarity search - Function
Glucosidase 2 subunit beta / Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. ...Glucosidase 2 subunit beta / Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Mannose-6-phosphate receptor binding domain superfamily / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glucosidase 2 subunit beta / alpha-glucosidase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSatoh, T. / Toshimori, T. / Noda, M. / Uchiyama, S. / Kato, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
JSPS KAKENHI25121730 Japan
JSPS KAKENHI15H02491 Japan
JSPS KAKENHI25102008 Japan
JSPS KAKENHI24249002 Japan
JST, PRESTO13417569 Japan
CitationJournal: Protein Sci. / Year: 2016
Title: Interaction mode between catalytic and regulatory subunits in glucosidase II involved in ER glycoprotein quality control.
Authors: Satoh, T. / Toshimori, T. / Noda, M. / Uchiyama, S. / Kato, K.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha glucosidase-like protein
B: Glucosidase 2 subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4575
Polymers126,2552
Non-polymers2023
Water11,800655
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-4 kcal/mol
Surface area37960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.716, 88.712, 173.103
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-1618-

HOH

21B-1175-

HOH

-
Components

#1: Protein Alpha glucosidase-like protein


Mass: 108501.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0064960 / Plasmid: PCOLD-GST (MODIFIED) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SG42
#2: Protein Glucosidase 2 subunit beta-like protein / Glucosidases


Mass: 17753.391 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0046400 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S9M2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 100 mM Bis-Tris (pH 6.5), 0.2 M ammonium phosphate

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 64671 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DKX

5dkx


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.189 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3317 5.1 %RANDOM
Rwork0.153 ---
obs0.155 61217 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.227 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2---0.79 Å20 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8373 0 10 655 9038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198633
X-RAY DIFFRACTIONr_bond_other_d0.0010.027885
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.93811714
X-RAY DIFFRACTIONr_angle_other_deg0.834318208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.21211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022060
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_it1.8742.344197
X-RAY DIFFRACTIONr_mcbond_other1.8732.3394196
X-RAY DIFFRACTIONr_mcangle_it2.9613.4975238
X-RAY DIFFRACTIONr_mcangle_other2.9613.4985239
X-RAY DIFFRACTIONr_scbond_it2.5942.5994436
X-RAY DIFFRACTIONr_scbond_other2.5942.64437
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2353.7736477
X-RAY DIFFRACTIONr_long_range_B_refined5.26123.6947960
X-RAY DIFFRACTIONr_long_range_B_other5.17423.6127708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 229 -
Rwork0.205 4195 -
obs--93.91 %

+
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