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- PDB-7kbj: Co-crystal structure of alpha glucosidase with compound 9 -

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Basic information

Entry
Database: PDB / ID: 7kbj
TitleCo-crystal structure of alpha glucosidase with compound 9
Components
  • (Neutral alpha-glucosidase AB Trypsin-cleaved Fragment ...) x 3
  • Glucosidase 2 subunit beta
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. / 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-WAV / Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 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
G: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
H: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
A: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
B: Glucosidase 2 subunit beta
I: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
J: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
C: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,80175
Polymers233,5008
Non-polymers6,30167
Water18,0691003
1
G: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
H: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
A: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,12237
Polymers116,7504
Non-polymers3,37233
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
J: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
C: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,67938
Polymers116,7504
Non-polymers2,92934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.652, 102.652, 238.908
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 or (resid 35 and (name...
21(chain C and (resid 34 through 184 or resid 246...
12(chain B and resid 36 through 117)
22(chain D and resid 36 through 117)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 34 or (resid 35 and (name...A34
121(chain A and (resid 34 or (resid 35 and (name...A35
131(chain A and (resid 34 or (resid 35 and (name...A33 - 966
141(chain A and (resid 34 or (resid 35 and (name...A33 - 966
151(chain A and (resid 34 or (resid 35 and (name...A33 - 966
161(chain A and (resid 34 or (resid 35 and (name...A33 - 966
211(chain C and (resid 34 through 184 or resid 246...C34 - 184
221(chain C and (resid 34 through 184 or resid 246...C246 - 252
231(chain C and (resid 34 through 184 or resid 246...C254 - 476
241(chain C and (resid 34 through 184 or resid 246...C478 - 527
251(chain C and (resid 34 through 184 or resid 246...C545 - 553
261(chain C and (resid 34 through 184 or resid 246...C560 - 578
271(chain C and (resid 34 through 184 or resid 246...C608 - 647
281(chain C and (resid 34 through 184 or resid 246...C579 - 606
291(chain C and (resid 34 through 184 or resid 246...C647 - 755
2101(chain C and (resid 34 through 184 or resid 246...C755 - 963
2111(chain C and (resid 34 through 184 or resid 246...C965 - 963
2121(chain C and (resid 34 through 184 or resid 246...C1001
2131(chain C and (resid 34 through 184 or resid 246...C2001 - 2501
2141(chain C and (resid 34 through 184 or resid 246...C2501 - 2701
2151(chain C and (resid 34 through 184 or resid 246...C3001 - 3301
112(chain B and resid 36 through 117)B36 - 117
212(chain D and resid 36 through 117)D36 - 117

NCS ensembles :
ID
1
2

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Components

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Neutral alpha-glucosidase AB Trypsin-cleaved Fragment ... , 3 types, 6 molecules GIHJAC

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


Mass: 20475.881 Da / Num. of mol.: 2 / Fragment: Trypsin-cleaved Fragment #1 / 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 Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 12052.347 Da / Num. of mol.: 2
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
#3: Protein Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 69898.688 Da / Num. of mol.: 2
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

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Protein , 1 types, 2 molecules BD

#4: Protein Glucosidase 2 subunit beta / 80K-H protein / Glucosidase II subunit beta / Protein kinase C substrate 60.1 kDa protein heavy chain / PKCSH


Mass: 14323.027 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, 1070 molecules

#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-WAV / (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[2-(2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethoxy)ethyl]amino}cyclohexane-1,2,3,4-tetrol


Mass: 446.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H30N6O8 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1003 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
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

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.21→42.09 Å / Num. obs: 140010 / % possible obs: 99.29 % / Redundancy: 9 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.1655 / Rpim(I) all: 0.0561 / Rrim(I) all: 0.175 / Net I/σ(I): 8.33
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.8132 / Num. unique obs: 13256 / Rpim(I) all: 0.4278 / Rrim(I) all: 0.9256 / % possible all: 93.27

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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→42.09 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 2031 1.45 %
Rwork0.167 137879 -
obs0.1674 139910 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.41 Å2 / Biso mean: 42.4273 Å2 / Biso min: 17.78 Å2
Refinement stepCycle: final / Resolution: 2.21→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15015 0 399 1004 16418
Biso mean--59.03 44.85 -
Num. residues----1877
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8235X-RAY DIFFRACTION6.519TORSIONAL
12C8235X-RAY DIFFRACTION6.519TORSIONAL
21B742X-RAY DIFFRACTION6.519TORSIONAL
22D742X-RAY DIFFRACTION6.519TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.260.32371300.28878358848890
2.26-2.320.2761300.25279301943199
2.32-2.380.24981380.220992879425100
2.38-2.450.25891300.20691899319100
2.45-2.530.26241340.211892089342100
2.53-2.620.23921420.197692989440100
2.62-2.730.23291360.189891979333100
2.73-2.850.2381340.186993219455100
2.85-30.23391310.185392379368100
3-3.190.22411320.168792319363100
3.19-3.430.20721440.157792779421100
3.43-3.780.16671340.149792539387100
3.78-4.330.1491360.137992589394100
4.33-5.450.1571360.129592379373100
5.45-42.090.17781440.156892279371100

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