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- PDB-7l9e: Crystal structure of apo-alpha glucosidase -

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Basic information

Entry
Database: PDB / ID: 7l9e
TitleCrystal structure of apo-alpha glucosidase
Components
  • (Neutral alpha-glucosidase AB Trypsin-cleaved Fragment ...) x 3
  • Glucosidase 2 subunit beta
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex
Function / homology
Function and homology information


mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development / carbohydrate binding / in utero embryonic development / carbohydrate metabolic process / intracellular membrane-bounded organelle / calcium ion binding / protein-containing complex binding / Golgi apparatus / endoplasmic reticulum / RNA binding
Similarity search - Function
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 / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / MRH domain ...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 / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / MRH domain / MRH domain profile. / 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 / EF hand / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Endoplasmic reticulum targeting sequence. / LDL receptor-like superfamily / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKarade, S.S. / Mariuzza, R.A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity.
Authors: Karade, S.S. / Hill, M.L. / Kiappes, J.L. / Manne, R. / Aakula, B. / Zitzmann, N. / Warfield, K.L. / Treston, A.M. / Mariuzza, R.A.
History
DepositionJan 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
F: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
A: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
B: Glucosidase 2 subunit beta
G: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
H: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
C: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,88942
Polymers233,5008
Non-polymers2,38934
Water12,250680
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.966, 102.966, 240.596
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 33 through 53 or (resid 54...
21(chain C and (resid 33 through 96 or resid 98...
12(chain B and (resid 34 through 58 or (resid 59...
22(chain D and (resid 34 through 45 or (resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 33 through 53 or (resid 54...A33 - 53
121(chain A and (resid 33 through 53 or (resid 54...A54
131(chain A and (resid 33 through 53 or (resid 54...A33 - 966
141(chain A and (resid 33 through 53 or (resid 54...A33 - 966
151(chain A and (resid 33 through 53 or (resid 54...A33 - 966
161(chain A and (resid 33 through 53 or (resid 54...A33 - 966
211(chain C and (resid 33 through 96 or resid 98...C33 - 96
221(chain C and (resid 33 through 96 or resid 98...C98 - 108
231(chain C and (resid 33 through 96 or resid 98...C109 - 110
241(chain C and (resid 33 through 96 or resid 98...C33 - 966
251(chain C and (resid 33 through 96 or resid 98...C33 - 966
261(chain C and (resid 33 through 96 or resid 98...C33 - 966
271(chain C and (resid 33 through 96 or resid 98...C33 - 966
112(chain B and (resid 34 through 58 or (resid 59...B34 - 58
122(chain B and (resid 34 through 58 or (resid 59...B59
132(chain B and (resid 34 through 58 or (resid 59...B33 - 202
142(chain B and (resid 34 through 58 or (resid 59...B33 - 202
152(chain B and (resid 34 through 58 or (resid 59...B33 - 202
162(chain B and (resid 34 through 58 or (resid 59...B33 - 202
212(chain D and (resid 34 through 45 or (resid 46...D34 - 45
222(chain D and (resid 34 through 45 or (resid 46...D46
232(chain D and (resid 34 through 45 or (resid 46...D34 - 202
242(chain D and (resid 34 through 45 or (resid 46...D34 - 202
252(chain D and (resid 34 through 45 or (resid 46...D34 - 202
262(chain D and (resid 34 through 45 or (resid 46...D34 - 202

NCS ensembles :
ID
1
2

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Components

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Neutral alpha-glucosidase AB Trypsin-cleaved Fragment ... , 3 types, 6 molecules EGFHAC

#1: Protein Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 20475.881 Da / Num. of mol.: 2 / Mutation: N97D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3, mannosyl-oligosaccharide alpha-1,3-glucosidase
#2: Protein Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 12052.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3, mannosyl-oligosaccharide alpha-1,3-glucosidase
#3: Protein Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 69898.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3, mannosyl-oligosaccharide alpha-1,3-glucosidase

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Protein , 1 types, 2 molecules BD

#4: Protein Glucosidase 2 subunit beta / 80K-H protein / Glucosidase II subunit beta / Protein kinase C substrate 60.1 kDa protein heavy chain / PKCSH


Mass: 14323.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08795

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Non-polymers , 6 types, 714 molecules

#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09 M NPS, 0.1 M Buffer System 1 (pH 7.0), 29% (v/v) P500MME P20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.997 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2019 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.29→47.33 Å / Num. obs: 128793 / % possible obs: 99.85 % / Redundancy: 2.8 % / Biso Wilson estimate: 44.16 Å2 / CC1/2: 0.967 / CC star: 0.991 / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.246
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.7 % / Num. unique obs: 12699 / CC1/2: 0.649 / CC star: 0.547 / % possible all: 99.73

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.29→47.33 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 2019 1.57 %
Rwork0.1796 126774 -
obs0.18 128793 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.82 Å2 / Biso mean: 49.8476 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.29→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14872 0 145 680 15697
Biso mean--63.77 50.68 -
Num. residues----1878
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7979X-RAY DIFFRACTION8.486TORSIONAL
12C7979X-RAY DIFFRACTION8.486TORSIONAL
21B712X-RAY DIFFRACTION8.486TORSIONAL
22D712X-RAY DIFFRACTION8.486TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.340.28451470.24219031917899
2.34-2.410.24321420.228789789120100
2.41-2.480.25491480.21290869234100
2.48-2.560.26441460.218790219167100
2.56-2.650.26751460.221791219267100
2.65-2.750.25821450.208390389183100
2.75-2.880.23351460.195490799225100
2.88-3.030.26241500.218690479197100
3.03-3.220.21631440.200390569200100
3.22-3.470.21171430.179290209163100
3.47-3.820.18521440.175591229266100
3.82-4.370.17321390.158390419180100
4.37-5.510.17841400.146290609200100
5.51-47.330.17691390.163290749213100

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