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- PDB-7kry: Co-crystal structure of alpha glucosidase with compound 11 -

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Basic information

Entry
Database: PDB / ID: 7kry
TitleCo-crystal structure of alpha glucosidase with compound 11
Components
  • Glucosidase 2 subunit betaGlucosidases
  • Neutral alpha-glucosidase AB
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex
Function / homology
Function and homology information


mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / 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 / melanosome / negative regulation of neuron projection development ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / 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 / melanosome / 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 / Golgi apparatus / 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-X8Y / Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionNov 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 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: Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
C: Neutral alpha-glucosidase AB
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,99520
Polymers340,9294
Non-polymers2,06616
Water9,242513
1
A: Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,54612
Polymers170,4652
Non-polymers1,08110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neutral alpha-glucosidase AB
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,4508
Polymers170,4652
Non-polymers9856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.923, 102.923, 240.215
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 67 or (resid 68...
12(chain B and (resid 34 through 44 or (resid 45...
22(chain D and (resid 34 through 37 or (resid 38...

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 67 or (resid 68...C33 - 67
221(chain C and (resid 33 through 67 or (resid 68...C68
231(chain C and (resid 33 through 67 or (resid 68...C33 - 966
241(chain C and (resid 33 through 67 or (resid 68...C33 - 966
251(chain C and (resid 33 through 67 or (resid 68...C33 - 966
261(chain C and (resid 33 through 67 or (resid 68...C33 - 966
112(chain B and (resid 34 through 44 or (resid 45...B34 - 44
122(chain B and (resid 34 through 44 or (resid 45...B45 - 46
132(chain B and (resid 34 through 44 or (resid 45...B34 - 117
142(chain B and (resid 34 through 44 or (resid 45...B34 - 117
152(chain B and (resid 34 through 44 or (resid 45...B34 - 117
162(chain B and (resid 34 through 44 or (resid 45...B34 - 117
212(chain D and (resid 34 through 37 or (resid 38...D34 - 37
222(chain D and (resid 34 through 37 or (resid 38...D38
232(chain D and (resid 34 through 37 or (resid 38...D34 - 201
242(chain D and (resid 34 through 37 or (resid 38...D34 - 201
252(chain D and (resid 34 through 37 or (resid 38...D34 - 201
262(chain D and (resid 34 through 37 or (resid 38...D34 - 201

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 108157.156 Da / Num. of mol.: 2 / Mutation: N97D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3, mannosyl-oligosaccharide alpha-1,3-glucosidase
#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: 62307.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Production host: Homo sapiens (human) / References: UniProt: O08795

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Non-polymers , 7 types, 529 molecules

#3: Chemical ChemComp-X8Y / (1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl)amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 454.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30N6O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
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: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 27, 2020
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→49.8 Å / Num. obs: 92459 / % possible obs: 99.96 % / Redundancy: 7.6 % / CC1/2: 0.989 / Rpim(I) all: 0.064 / Net I/σ(I): 11.21
Reflection shellResolution: 2.55→2.644 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 9308 / CC1/2: 0.553 / Rpim(I) all: 0.509 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.55→49.8 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 1989 2.15 %
Rwork0.181 90460 -
obs0.1818 92449 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.37 Å2 / Biso mean: 51.9189 Å2 / Biso min: 29.75 Å2
Refinement stepCycle: final / Resolution: 2.55→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14896 0 131 513 15540
Biso mean--60.19 49.2 -
Num. residues----1879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715518
X-RAY DIFFRACTIONf_angle_d0.98821143
X-RAY DIFFRACTIONf_dihedral_angle_d18.845617
X-RAY DIFFRACTIONf_chiral_restr0.0582227
X-RAY DIFFRACTIONf_plane_restr0.0072765
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8145X-RAY DIFFRACTION7.813TORSIONAL
12C8145X-RAY DIFFRACTION7.813TORSIONAL
21B704X-RAY DIFFRACTION7.813TORSIONAL
22D704X-RAY DIFFRACTION7.813TORSIONAL
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
2.55-2.620.32291390.279464836622
2.62-2.690.30461380.255364206558
2.69-2.770.29451520.239164756627
2.77-2.860.29981390.24465206659
2.86-2.960.27511420.237764376579
2.96-3.080.27651380.219164466584
3.08-3.220.24661400.20164806620
3.22-3.390.23761440.209364126556
3.39-3.60.21751480.186664726620
3.6-3.880.22281500.169664656615
3.88-4.270.19061260.155265016627
4.27-4.880.17761520.142564336585
4.88-6.150.18251360.156764636599
6.15-49.80.17931450.151564536598

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