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- PDB-7jty: Co-crystal structure of alpha glucosidase with compound 1 -

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Basic information

Entry
Database: PDB / ID: 7jty
TitleCo-crystal structure of alpha glucosidase with compound 1
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 / Chem-VND / 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: 2.21 Å
AuthorsKarade, S.S. / Mariuzza, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
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
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 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)346,13927
Polymers344,2114
Non-polymers1,92823
Water15,889882
1
A: Alpha glucosidase 2 alpha neutral subunit
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,98212
Polymers172,1062
Non-polymers87610
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)173,15815
Polymers172,1062
Non-polymers1,05213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.561, 102.561, 239.559
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 34 through 53 or (resid 54...
21(chain C and (resid 34 through 109 or (resid 110...
12(chain B and (resid 35 through 42 or (resid 43...
22(chain D and (resid 35 through 81 or (resid 82...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 34 through 53 or (resid 54...A34 - 53
121(chain A and (resid 34 through 53 or (resid 54...A54
131(chain A and (resid 34 through 53 or (resid 54...A34 - 966
141(chain A and (resid 34 through 53 or (resid 54...A34 - 966
151(chain A and (resid 34 through 53 or (resid 54...A34 - 966
161(chain A and (resid 34 through 53 or (resid 54...A34 - 966
211(chain C and (resid 34 through 109 or (resid 110...C34 - 109
221(chain C and (resid 34 through 109 or (resid 110...C110
231(chain C and (resid 34 through 109 or (resid 110...C33 - 966
241(chain C and (resid 34 through 109 or (resid 110...C33 - 966
251(chain C and (resid 34 through 109 or (resid 110...C33 - 966
261(chain C and (resid 34 through 109 or (resid 110...C33 - 966
112(chain B and (resid 35 through 42 or (resid 43...B35 - 42
122(chain B and (resid 35 through 42 or (resid 43...B43 - 44
132(chain B and (resid 35 through 42 or (resid 43...B35 - 202
142(chain B and (resid 35 through 42 or (resid 43...B35 - 202
152(chain B and (resid 35 through 42 or (resid 43...B35 - 202
162(chain B and (resid 35 through 42 or (resid 43...B35 - 202
212(chain D and (resid 35 through 81 or (resid 82...D35 - 81
222(chain D and (resid 35 through 81 or (resid 82...D82 - 83
232(chain D and (resid 35 through 81 or (resid 82...D33 - 202
242(chain D and (resid 35 through 81 or (resid 82...D33 - 202
252(chain D and (resid 35 through 81 or (resid 82...D33 - 202
262(chain D and (resid 35 through 81 or (resid 82...D33 - 202

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 , 6 types, 905 molecules

#3: Chemical ChemComp-VND / (1S,2S,3R,4S,5S)-5-(butylamino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 249.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Description: obtained diamond shaped crystals after seeding.
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09M NPS, 0.1M Buffer System 1 pH7.0, 29.0%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 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
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: 2.21→42.17 Å / Num. obs: 140781 / % possible obs: 99.97 % / Redundancy: 8.4 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1091 / Rpim(I) all: 0.03977 / Rrim(I) all: 0.1162 / Net I/σ(I): 10.38
Reflection shellResolution: 2.21→2.291 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.8133 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 14113 / CC1/2: 0.695 / CC star: 0.906 / Rpim(I) all: 0.8133 / Rrim(I) all: 0.8773 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.21→42.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 1992 1.41 %
Rwork0.1697 138789 -
obs0.1702 140781 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.42 Å2 / Biso mean: 42.8243 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 2.21→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14883 0 114 883 15880
Biso mean--54.74 46.09 -
Num. residues----1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615499
X-RAY DIFFRACTIONf_angle_d0.87721121
X-RAY DIFFRACTIONf_dihedral_angle_d20.1965616
X-RAY DIFFRACTIONf_chiral_restr0.0542228
X-RAY DIFFRACTIONf_plane_restr0.0052761
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8045X-RAY DIFFRACTION7.133TORSIONAL
12C8045X-RAY DIFFRACTION7.133TORSIONAL
21B709X-RAY DIFFRACTION7.133TORSIONAL
22D709X-RAY DIFFRACTION7.133TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.21-2.270.29191400.251994910089
2.27-2.330.27221440.2199995210096
2.33-2.40.24331420.19998539995
2.4-2.470.24061400.1936988610026
2.47-2.560.2151440.1964998610130
2.56-2.670.26621460.181798009946
2.67-2.790.23121420.1745999610138
2.79-2.930.21351420.1962991510057
2.93-3.120.21211440.1784990910053
3.12-3.360.20151440.1641990910053
3.36-3.70.21191420.1586988810030
3.7-4.230.17651460.1532992310069
4.23-5.330.16541390.142991810057
5.33-42.170.17891370.1686990510042

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