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- PDB-7k9o: Co-crystal structure of alpha glucosidase with compound 3 -

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Basic information

Entry
Database: PDB / ID: 7k9o
TitleCo-crystal structure of alpha glucosidase with compound 3
Components
  • Alpha glucosidase 2 alpha neutral subunit
  • Glucosidase 2 subunit betaGlucosidases
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex
Function / homology
Function and homology information


glucan 1,3-alpha-glucosidase activity / glucosidase II complex / 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 / negative regulation of neuron projection development / carbohydrate binding / in utero embryonic development / carbohydrate metabolic process ...glucan 1,3-alpha-glucosidase activity / glucosidase II complex / 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 / 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 / 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 / TRIETHYLENE GLYCOL / Chem-W9P / Alpha glucosidase 2 alpha neutral subunit / Glucosidase 2 subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 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
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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 1.3Oct 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
A: Alpha glucosidase 2 alpha neutral subunit
B: Glucosidase 2 subunit beta
C: Alpha glucosidase 2 alpha neutral subunit
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,98145
Polymers344,2114
Non-polymers3,77041
Water11,151619
1
A: Alpha glucosidase 2 alpha neutral subunit
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,21725
Polymers172,1062
Non-polymers2,11123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha glucosidase 2 alpha neutral subunit
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,76420
Polymers172,1062
Non-polymers1,65918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.716, 102.716, 239.625
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 70 or (resid 71...
12(chain B and (resid 35 through 116 or (resid 117...
22(chain D and (resid 35 through 202 or resid 301))

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 70 or (resid 71...C33 - 70
221(chain C and (resid 33 through 70 or (resid 71...C71 - 73
231(chain C and (resid 33 through 70 or (resid 71...C33 - 966
241(chain C and (resid 33 through 70 or (resid 71...C33 - 966
251(chain C and (resid 33 through 70 or (resid 71...C33 - 966
261(chain C and (resid 33 through 70 or (resid 71...C33 - 966
112(chain B and (resid 35 through 116 or (resid 117...B35 - 116
122(chain B and (resid 35 through 116 or (resid 117...B117
132(chain B and (resid 35 through 116 or (resid 117...B35 - 117
142(chain B and (resid 35 through 116 or (resid 117...B35 - 117
152(chain B and (resid 35 through 116 or (resid 117...B35 - 117
162(chain B and (resid 35 through 116 or (resid 117...B35 - 117
212(chain D and (resid 35 through 202 or resid 301))D35 - 202
222(chain D and (resid 35 through 202 or resid 301))D301

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Alpha glucosidase 2 alpha neutral subunit / Neutral alpha-glucosidase AB


Mass: 110654.062 Da / Num. of mol.: 2 / Mutation: N97D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: A1A4T2
#2: Protein Glucosidase 2 subunit beta / Glucosidases / 80K-H protein / Glucosidase II subunit beta / Protein kinase C substrate 60.1 kDa protein heavy chain / PKCSH


Mass: 61451.488 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 , 7 types, 660 molecules

#3: Chemical ChemComp-W9P / (1~{S},2~{S},3~{R},4~{S},5~{S})-1-(hydroxymethyl)-5-[6-[[2-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-4-(1,2,3,4-tetrazol-1-yl)phenyl]amino]hexylamino]cyclohexane-1,2,3,4-tetrol


Mass: 481.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31N7O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09M NPS, 0.1M Buffer System 1 pH7.0, 29%v/v P500MME_P20K (Morpheus screen, condition C1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2020
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.302→39.938 Å / Num. obs: 125193 / % possible obs: 99.89 % / Redundancy: 7.2 % / Biso Wilson estimate: 45.37 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1386 / Rpim(I) all: 0.05381 / Rrim(I) all: 0.1489 / Net I/σ(I): 8.09
Reflection shellResolution: 2.302→2.384 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.9136 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 12513 / CC1/2: 0.445 / CC star: 0.785 / Rpim(I) all: 0.4163 / Rrim(I) all: 1.007 / % possible all: 99.17

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.302→39.938 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 2012 1.61 %
Rwork0.2099 123176 -
obs0.2103 125188 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.92 Å2 / Biso mean: 48.9425 Å2 / Biso min: 22.28 Å2
Refinement stepCycle: final / Resolution: 2.302→39.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14969 0 243 623 15835
Biso mean--54.49 49.16 -
Num. residues----1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315767
X-RAY DIFFRACTIONf_angle_d0.68221436
X-RAY DIFFRACTIONf_dihedral_angle_d14.8489325
X-RAY DIFFRACTIONf_chiral_restr0.0472246
X-RAY DIFFRACTIONf_plane_restr0.0042789
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8211X-RAY DIFFRACTION6.207TORSIONAL
12C8211X-RAY DIFFRACTION6.207TORSIONAL
21B752X-RAY DIFFRACTION6.207TORSIONAL
22D752X-RAY DIFFRACTION6.207TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3021-2.35970.30951430.3035867399
2.3597-2.42350.28881380.26798864100
2.4235-2.49480.28991420.24948788100
2.4948-2.57530.27181420.24598849100
2.5753-2.66730.2951460.23618757100
2.6673-2.77410.29121460.23238845100
2.7741-2.90030.26431400.22818802100
2.9003-3.05320.2741420.22538769100
3.0532-3.24440.23431440.21218833100
3.2444-3.49480.22361520.20648778100
3.4948-3.84620.211480.20128796100
3.8462-4.40220.2221390.18978810100
4.4022-5.54390.22811420.18898818100
5.5439-39.9380.2151480.19778794100

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