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- PDB-7kb8: Co-crystal structure of alpha glucosidase with compound 8 -

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Basic information

Entry
Database: PDB / ID: 7kb8
TitleCo-crystal structure of alpha glucosidase with compound 8
Components
  • Glucosidase 2 subunit betaGlucosidases
  • Isoform 2 of Neutral alpha-glucosidase AB
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex
Function / homology
Function and homology information


mannosyl-oligosaccharide alpha-1,3-glucosidase / 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 / in utero embryonic development / intracellular membrane-bounded organelle / calcium ion binding ...mannosyl-oligosaccharide alpha-1,3-glucosidase / 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 / in utero embryonic development / 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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / EF hand / Endoplasmic reticulum targeting sequence. ...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 / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / EF hand / Endoplasmic reticulum targeting sequence. / LDL receptor-like superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-WA7 / Glucosidase 2 subunit beta / Isoform 2 of Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.385 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 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 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: Isoform 2 of Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
C: Isoform 2 of Neutral alpha-glucosidase AB
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,97159
Polymers345,9234
Non-polymers5,04855
Water10,629590
1
A: Isoform 2 of Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,55628
Polymers172,9612
Non-polymers2,59526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Isoform 2 of Neutral alpha-glucosidase AB
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,41431
Polymers172,9612
Non-polymers2,45329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.782, 102.782, 240.124
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 34 or (resid 35...
21(chain C and (resid 33 through 184 or resid 246...
12(chain B and (resid 31 through 32 or (resid 33...
22(chain D and (resid 31 through 42 or (resid 43...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 33 through 34 or (resid 35...A33 - 34
121(chain A and (resid 33 through 34 or (resid 35...A35
131(chain A and (resid 33 through 34 or (resid 35...A33 - 966
141(chain A and (resid 33 through 34 or (resid 35...A33 - 966
151(chain A and (resid 33 through 34 or (resid 35...A33 - 966
161(chain A and (resid 33 through 34 or (resid 35...A33 - 966
211(chain C and (resid 33 through 184 or resid 246...C33 - 184
221(chain C and (resid 33 through 184 or resid 246...C246 - 476
231(chain C and (resid 33 through 184 or resid 246...C478 - 527
241(chain C and (resid 33 through 184 or resid 246...C545
251(chain C and (resid 33 through 184 or resid 246...C33 - 966
261(chain C and (resid 33 through 184 or resid 246...C579 - 645
271(chain C and (resid 33 through 184 or resid 246...C33 - 966
281(chain C and (resid 33 through 184 or resid 246...C928
291(chain C and (resid 33 through 184 or resid 246...C33 - 966
2101(chain C and (resid 33 through 184 or resid 246...C33 - 966
2111(chain C and (resid 33 through 184 or resid 246...C33 - 966
2121(chain C and (resid 33 through 184 or resid 246...C33 - 966
2131(chain C and (resid 33 through 184 or resid 246...C33 - 966
112(chain B and (resid 31 through 32 or (resid 33...B31 - 32
122(chain B and (resid 31 through 32 or (resid 33...B33 - 35
132(chain B and (resid 31 through 32 or (resid 33...B31 - 601
142(chain B and (resid 31 through 32 or (resid 33...B31 - 601
152(chain B and (resid 31 through 32 or (resid 33...B31 - 601
162(chain B and (resid 31 through 32 or (resid 33...B31 - 601
172(chain B and (resid 31 through 32 or (resid 33...B48
182(chain B and (resid 31 through 32 or (resid 33...B31 - 601
192(chain B and (resid 31 through 32 or (resid 33...B31 - 601
1102(chain B and (resid 31 through 32 or (resid 33...B31 - 601
1112(chain B and (resid 31 through 32 or (resid 33...B31 - 601
212(chain D and (resid 31 through 42 or (resid 43...D31 - 42
222(chain D and (resid 31 through 42 or (resid 43...D43 - 45
232(chain D and (resid 31 through 42 or (resid 43...D31 - 401
242(chain D and (resid 31 through 42 or (resid 43...D31 - 401
252(chain D and (resid 31 through 42 or (resid 43...D31 - 401
262(chain D and (resid 31 through 42 or (resid 43...D31 - 401

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

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


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, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3-2, 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 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08795

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Non-polymers , 7 types, 645 molecules

#3: Chemical ChemComp-WA7 / (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-[(4-{[2-nitro-4-(triazan-1-yl)phenyl]amino}butyl)amino]cyclohexane-1,2,3,4-tetrol


Mass: 426.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H26N6O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
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: 2.385→40.021 Å / Num. obs: 112724 / % possible obs: 99.72 % / Redundancy: 6.6 % / Biso Wilson estimate: 48.18 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1151 / Rpim(I) all: 0.04801 / Rrim(I) all: 0.1249 / Net I/σ(I): 8.42
Reflection shellResolution: 2.385→2.47 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.9231 / Num. unique obs: 11064 / CC1/2: 0.537 / CC star: 0.836 / Rpim(I) all: 0.4207 / Rrim(I) all: 1.02 / % possible all: 97.93

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHENIX1.14_3228phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.385→40.021 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 1979 1.76 %
Rwork0.1736 110728 -
obs0.1743 112707 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.24 Å2 / Biso mean: 50.8036 Å2 / Biso min: 23.56 Å2
Refinement stepCycle: final / Resolution: 2.385→40.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14992 0 325 592 15909
Biso mean--63.88 49.54 -
Num. residues----1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715810
X-RAY DIFFRACTIONf_angle_d0.91921442
X-RAY DIFFRACTIONf_dihedral_angle_d15.0359307
X-RAY DIFFRACTIONf_chiral_restr0.0552240
X-RAY DIFFRACTIONf_plane_restr0.0062783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8215X-RAY DIFFRACTION7.51TORSIONAL
12C8215X-RAY DIFFRACTION7.51TORSIONAL
21B780X-RAY DIFFRACTION7.51TORSIONAL
22D780X-RAY DIFFRACTION7.51TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.385-2.44420.30511400.268761296
2.4442-2.51030.3211460.23987961100
2.5103-2.58410.26181380.21377918100
2.5841-2.66750.23011420.21177921100
2.6675-2.76280.27791400.20377894100
2.7628-2.87340.23691460.19888034100
2.8734-3.00420.23861440.19567894100
3.0042-3.16250.25141440.1867889100
3.1625-3.36050.21291380.18757983100
3.3605-3.61990.19961430.17157892100
3.6199-3.98380.20431340.1657966100
3.9838-4.55960.17961480.14847887100
4.5596-5.74190.1821380.14837975100
5.7419-40.0210.18161380.15657902100

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