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- PDB-7k9q: Co-crystal structure of alpha glucosidase with compound 4 -

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Basic information

Entry
Database: PDB / ID: 7k9q
TitleCo-crystal structure of alpha glucosidase with compound 4
Components
  • Alpha glucosidase 2 alpha neutral subunit
  • Glucosidase 2 subunit beta
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


glucan 1,3-alpha-glucosidase activity / nitrogen cycle metabolic process / 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 ...glucan 1,3-alpha-glucosidase activity / nitrogen cycle metabolic process / 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. / 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 / : / 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-W9S / 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: 2.3 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
Revision 1.4Nov 6, 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

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)349,23964
Polymers344,2114
Non-polymers5,02760
Water15,691871
1
A: Alpha glucosidase 2 alpha neutral subunit
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,21640
Polymers172,1062
Non-polymers3,11038
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)174,02324
Polymers172,1062
Non-polymers1,91722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.876, 102.876, 241.696
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 78 or (resid 79...
12(chain B and ((resid 31 through 32 and (name N...
22(chain D and (resid 31 through 40 or (resid 41...

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
111VALVALILEILE(chain A and (resid 33 through 53 or (resid 54...AA33 - 5332 - 52
121ARGARGARGARG(chain A and (resid 33 through 53 or (resid 54...AA5453
131VALVALARGARG(chain A and (resid 33 through 53 or (resid 54...AA33 - 96632 - 965
141VALVALARGARG(chain A and (resid 33 through 53 or (resid 54...AA33 - 96632 - 965
151VALVALARGARG(chain A and (resid 33 through 53 or (resid 54...AA33 - 96632 - 965
161VALVALARGARG(chain A and (resid 33 through 53 or (resid 54...AA33 - 96632 - 965
211VALVALLEULEU(chain C and (resid 33 through 78 or (resid 79...CC33 - 7832 - 77
221ILEILEILEILE(chain C and (resid 33 through 78 or (resid 79...CC7978
231VALVALARGARG(chain C and (resid 33 through 78 or (resid 79...CC33 - 96632 - 965
241VALVALARGARG(chain C and (resid 33 through 78 or (resid 79...CC33 - 96632 - 965
251VALVALARGARG(chain C and (resid 33 through 78 or (resid 79...CC33 - 96632 - 965
261VALVALARGARG(chain C and (resid 33 through 78 or (resid 79...CC33 - 96632 - 965
112TYRTYRGLUGLU(chain B and ((resid 31 through 32 and (name N...BB31 - 3248 - 49
122TYRTYRARGARG(chain B and ((resid 31 through 32 and (name N...BB31 - 11748 - 134
132TYRTYRARGARG(chain B and ((resid 31 through 32 and (name N...BB31 - 11748 - 134
142TYRTYRARGARG(chain B and ((resid 31 through 32 and (name N...BB31 - 11748 - 134
152TYRTYRARGARG(chain B and ((resid 31 through 32 and (name N...BB31 - 11748 - 134
212TYRTYRLEULEU(chain D and (resid 31 through 40 or (resid 41...DD31 - 4048 - 57
222ASPASPASPASP(chain D and (resid 31 through 40 or (resid 41...DD4158
232PHEPHEARGARG(chain D and (resid 31 through 40 or (resid 41...DD30 - 11747 - 134
242PHEPHEARGARG(chain D and (resid 31 through 40 or (resid 41...DD30 - 11747 - 134
252PHEPHEARGARG(chain D and (resid 31 through 40 or (resid 41...DD30 - 11747 - 134
262PHEPHEARGARG(chain D and (resid 31 through 40 or (resid 41...DD30 - 11747 - 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 / 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, 931 molecules

#3: Chemical ChemComp-W9S / (1S,2S,3R,4S,5S)-5-amino-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 193.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / 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.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 871 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
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 / 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: 2.3→42.49 Å / Num. obs: 126356 / % possible obs: 99.86 % / Redundancy: 8.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.048 / Rrim(I) all: 0.14 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.386 Å / Rmerge(I) obs: 1.105 / Num. unique obs: 12577 / CC1/2: 0.608 / Rpim(I) all: 0.437 / Rrim(I) all: 1.19 / % possible all: 99.31

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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: 2.3→42.49 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 1995 1.58 %
Rwork0.172 124349 -
obs0.1724 126344 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.61 Å2 / Biso mean: 45.7062 Å2 / Biso min: 20.75 Å2
Refinement stepCycle: final / Resolution: 2.3→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15002 0 315 873 16190
Biso mean--57.14 46.84 -
Num. residues----1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415809
X-RAY DIFFRACTIONf_angle_d0.74721446
X-RAY DIFFRACTIONf_dihedral_angle_d19.2735755
X-RAY DIFFRACTIONf_chiral_restr0.0492243
X-RAY DIFFRACTIONf_plane_restr0.0052788
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8057X-RAY DIFFRACTION7.518TORSIONAL
12C8057X-RAY DIFFRACTION7.518TORSIONAL
21B755X-RAY DIFFRACTION7.518TORSIONAL
22D755X-RAY DIFFRACTION7.518TORSIONAL
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 (%)
2.3-2.360.2781440.26358734887899
2.36-2.420.27761400.236889229062100
2.42-2.50.2781360.218889519087100
2.5-2.580.25951440.217488919035100
2.58-2.670.24011400.219988809020100
2.67-2.780.22111500.202589039053100
2.78-2.90.23651380.192588338971100
2.9-3.050.22111460.198489419087100
3.06-3.250.21431400.186588899029100
3.25-3.50.19651500.168488989048100
3.5-3.850.19181380.15888709008100
3.85-4.40.16511420.145388769018100
4.4-5.550.16051430.137888769019100
5.55-42.490.16861440.153588859029100

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