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- PDB-7k9n: Co-crystal structure of alpha glucosidase with compound 2 -

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Basic information

Entry
Database: PDB / ID: 7k9n
TitleCo-crystal structure of alpha glucosidase with compound 2
Components
  • Alpha glucosidase 2 alpha neutral subunit
  • Glucosidase 2 subunit betaGlucosidases
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex / HYDROLASE-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-W9G / 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: 2.07 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)349,60961
Polymers344,2114
Non-polymers5,39857
Water20,2671125
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A: Alpha glucosidase 2 alpha neutral subunit
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,29036
Polymers172,1062
Non-polymers3,18434
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)174,31925
Polymers172,1062
Non-polymers2,21323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.788, 102.788, 240.902
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 36 or resid 38...
21(chain C and (resid 33 through 36 or resid 38...
12(chain B and (resid 31 through 116 or (resid 117...
22(chain D and (resid 31 through 45 or (resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALSERSER(chain A and (resid 33 through 36 or resid 38...AA33 - 3632 - 35
121PHEPHEILEILE(chain A and (resid 33 through 36 or resid 38...AA38 - 5337 - 52
131ARGARGARGARG(chain A and (resid 33 through 36 or resid 38...AA5453
141VALVALARGARG(chain A and (resid 33 through 36 or resid 38...AA33 - 96632 - 965
151VALVALARGARG(chain A and (resid 33 through 36 or resid 38...AA33 - 96632 - 965
161VALVALARGARG(chain A and (resid 33 through 36 or resid 38...AA33 - 96632 - 965
171VALVALARGARG(chain A and (resid 33 through 36 or resid 38...AA33 - 96632 - 965
211VALVALSERSER(chain C and (resid 33 through 36 or resid 38...CC33 - 3632 - 35
221PHEPHELYSLYS(chain C and (resid 33 through 36 or resid 38...CC38 - 9637 - 95
231METMETGLYGLY(chain C and (resid 33 through 36 or resid 38...CC98 - 13297 - 131
241VALVALARGARG(chain C and (resid 33 through 36 or resid 38...CC33 - 96632 - 965
251VALVALARGARG(chain C and (resid 33 through 36 or resid 38...CC33 - 96632 - 965
261VALVALARGARG(chain C and (resid 33 through 36 or resid 38...CC33 - 96632 - 965
271VALVALARGARG(chain C and (resid 33 through 36 or resid 38...CC33 - 96632 - 965
281VALVALARGARG(chain C and (resid 33 through 36 or resid 38...CC33 - 96632 - 965
291VALVALARGARG(chain C and (resid 33 through 36 or resid 38...CC33 - 96632 - 965
112TYRTYRCYSCYS(chain B and (resid 31 through 116 or (resid 117...BB31 - 11648 - 133
122ARGARGARGARG(chain B and (resid 31 through 116 or (resid 117...BB117134
132TYRTYRARGARG(chain B and (resid 31 through 116 or (resid 117...BB31 - 11748 - 134
142TYRTYRARGARG(chain B and (resid 31 through 116 or (resid 117...BB31 - 11748 - 134
152TYRTYRARGARG(chain B and (resid 31 through 116 or (resid 117...BB31 - 11748 - 134
162TYRTYRARGARG(chain B and (resid 31 through 116 or (resid 117...BB31 - 11748 - 134
172TYRTYRARGARG(chain B and (resid 31 through 116 or (resid 117...BB31 - 11748 - 134
212TYRTYRTHRTHR(chain D and (resid 31 through 45 or (resid 46...DD31 - 4548 - 62
222ILEILEILEILE(chain D and (resid 31 through 45 or (resid 46...DD4663
232TYRTYRARGARG(chain D and (resid 31 through 45 or (resid 46...DD31 - 11748 - 134
242TYRTYRARGARG(chain D and (resid 31 through 45 or (resid 46...DD31 - 11748 - 134
252TYRTYRARGARG(chain D and (resid 31 through 45 or (resid 46...DD31 - 11748 - 134
262TYRTYRARGARG(chain D and (resid 31 through 45 or (resid 46...DD31 - 11748 - 134

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 , 8 types, 1182 molecules

#3: Chemical ChemComp-W9G / (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(9-methoxynonyl)amino]cyclohexane-1,2,3,4-tetrol


Mass: 349.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H35NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / 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 / Water


Mass: 18.015 Da / Num. of mol.: 1125 / 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: 2.13 Å3/Da / Density % sol: 42.38 % / 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 pH 7.0, 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: 2.07→41.75 Å / Num. obs: 172944 / % possible obs: 99.86 % / Redundancy: 7.9 % / Biso Wilson estimate: 35.16 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1132 / Rpim(I) all: 0.04264 / Rrim(I) all: 0.1212 / Net I/σ(I): 10.1
Reflection shellResolution: 2.07→2.146 Å / Redundancy: 7 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 17243 / CC1/2: 0.603 / CC star: 0.867 / Rpim(I) all: 0.43 / Rrim(I) all: 1.156 / % possible all: 99.3

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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: 2.07→41.75 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 2009 1.16 %
Rwork0.1698 170894 -
obs0.1701 172903 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.57 Å2 / Biso mean: 40.6861 Å2 / Biso min: 16.07 Å2
Refinement stepCycle: final / Resolution: 2.07→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14889 0 339 1126 16354
Biso mean--55.8 45.04 -
Num. residues----1883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615750
X-RAY DIFFRACTIONf_angle_d0.87521389
X-RAY DIFFRACTIONf_dihedral_angle_d19.1255732
X-RAY DIFFRACTIONf_chiral_restr0.0542249
X-RAY DIFFRACTIONf_plane_restr0.0062772
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7944X-RAY DIFFRACTION7.074TORSIONAL
12C7944X-RAY DIFFRACTION7.074TORSIONAL
21B733X-RAY DIFFRACTION7.074TORSIONAL
22D733X-RAY DIFFRACTION7.074TORSIONAL
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 (%)
2.07-2.120.28891400.2701121411228199
2.12-2.180.26511480.23891221312361100
2.18-2.240.26661480.21271223912387100
2.24-2.320.25771460.20741218412330100
2.32-2.40.23581460.20481226112407100
2.4-2.50.21631440.19621221812362100
2.5-2.610.21471440.1781217812322100
2.61-2.750.22041460.19741221012356100
2.75-2.920.19041380.18821224812386100
2.92-3.140.20091390.17081216712306100
3.14-3.460.2021440.16391225812402100
3.46-3.960.18321430.15191221012353100
3.96-4.990.13911380.13061216512303100
4.99-41.750.1751450.15521220212347100

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