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- PDB-7k9t: Co-crystal structure of alpha glucosidase with compound 5 -

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Basic information

Entry
Database: PDB / ID: 7k9t
TitleCo-crystal structure of alpha glucosidase with compound 5
Components
  • Alpha glucosidase 2 alpha neutral subunit
  • Glucosidase 2 subunit beta
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex
Function / homology
Function and homology information


glucan 1,3-alpha-glucosidase activity / mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / nitrogen cycle metabolic process / 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 ...glucan 1,3-alpha-glucosidase activity / mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / nitrogen cycle metabolic process / 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. / Mannose-6-phosphate receptor binding domain superfamily ...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. / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / EF hand / : / Glycosyl hydrolase family 31 C-terminal domain / 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-W9V / Neutral alpha-glucosidase AB / Glucosidase 2 subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)350,75665
Polymers344,2114
Non-polymers6,54561
Water17,673981
1
A: Alpha glucosidase 2 alpha neutral subunit
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,67735
Polymers172,1062
Non-polymers3,57233
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)175,07930
Polymers172,1062
Non-polymers2,97328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.870, 102.870, 240.653
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 472 or resid 474...
21(chain C and (resid 34 through 108 or (resid 109...
12(chain B and (resid 35 through 202 or resid 301))
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 472 or resid 474...A34 - 472
121(chain A and (resid 34 through 472 or resid 474...A474 - 476
131(chain A and (resid 34 through 472 or resid 474...A478 - 527
141(chain A and (resid 34 through 472 or resid 474...A529 - 538
151(chain A and (resid 34 through 472 or resid 474...A560 - 578
161(chain A and (resid 34 through 472 or resid 474...A579 - 647
171(chain A and (resid 34 through 472 or resid 474...A795
181(chain A and (resid 34 through 472 or resid 474...A647 - 794
191(chain A and (resid 34 through 472 or resid 474...A34 - 966
1101(chain A and (resid 34 through 472 or resid 474...A34 - 966
1111(chain A and (resid 34 through 472 or resid 474...A34 - 966
1121(chain A and (resid 34 through 472 or resid 474...A34 - 966
1131(chain A and (resid 34 through 472 or resid 474...A34 - 966
211(chain C and (resid 34 through 108 or (resid 109...C34 - 108
221(chain C and (resid 34 through 108 or (resid 109...C109 - 110
231(chain C and (resid 34 through 108 or (resid 109...C33 - 966
241(chain C and (resid 34 through 108 or (resid 109...C33 - 966
251(chain C and (resid 34 through 108 or (resid 109...C33 - 966
261(chain C and (resid 34 through 108 or (resid 109...C33 - 966
112(chain B and (resid 35 through 202 or resid 301))B35 - 202
122(chain B and (resid 35 through 202 or resid 301))B301
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...D31 - 117
242(chain D and (resid 35 through 81 or (resid 82...D31 - 117
252(chain D and (resid 35 through 81 or (resid 82...D31 - 117
262(chain D and (resid 35 through 81 or (resid 82...D31 - 117

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 / 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 , 9 types, 1042 molecules

#3: Chemical ChemComp-W9V / (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[(5Z)-6-{[2-nitro-4-(2H-1,2,3-triazol-2-yl)phenyl]amino}hex-5-en-1-yl]amino}cyclohexane-1,2,3,4-tetrol


Mass: 480.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32N6O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 981 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09M NPS, 0.1M Buffer System 1 pH 7.0, 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 / 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: 2.1→42.35 Å / Num. obs: 165417 / % possible obs: 99.93 % / Redundancy: 8.2 % / Biso Wilson estimate: 35.78 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1298 / Rpim(I) all: 0.04788 / Rrim(I) all: 0.1385 / Net I/σ(I): 9.53
Reflection shellResolution: 2.1→2.178 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 16531 / CC1/2: 0.579 / CC star: 0.856 / Rpim(I) all: 0.4638 / Rrim(I) all: 1.231 / % possible all: 99.73

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Processing

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

5f0e


Resolution: 2.1→42.35 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1915 2002 1.21 %
Rwork0.1706 163371 -
obs0.1709 165373 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.33 Å2 / Biso mean: 43.9064 Å2 / Biso min: 17.17 Å2
Refinement stepCycle: final / Resolution: 2.1→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14989 0 421 983 16393
Biso mean--65.51 47.16 -
Num. residues----1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415875
X-RAY DIFFRACTIONf_angle_d0.87321502
X-RAY DIFFRACTIONf_dihedral_angle_d19.7925818
X-RAY DIFFRACTIONf_chiral_restr0.082237
X-RAY DIFFRACTIONf_plane_restr0.0042782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8237X-RAY DIFFRACTION6.504TORSIONAL
12C8237X-RAY DIFFRACTION6.504TORSIONAL
21B754X-RAY DIFFRACTION6.504TORSIONAL
22D754X-RAY DIFFRACTION6.504TORSIONAL
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
2.1-2.160.30631360.27331163711773
2.16-2.210.26941520.23461164011792
2.21-2.280.26511420.21271173311875
2.28-2.350.23111500.21161162611776
2.35-2.440.2761400.21151172511865
2.44-2.530.20481440.19221163011774
2.53-2.650.20761400.17541170211842
2.65-2.790.2211380.19871169611834
2.79-2.960.21461370.19081168911826
2.96-3.190.19131500.17041162911779
3.19-3.510.18581480.16521166611814
3.51-4.020.16061460.15381166211808
4.02-5.070.1441380.13251168811826
5.07-42.350.1741410.15271164811789

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