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- PDB-5h9o: Complex of Murine endoplasmic reticulum alpha-glucosidase II with... -

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Basic information

Entry
Database: PDB / ID: 5h9o
TitleComplex of Murine endoplasmic reticulum alpha-glucosidase II with D-Glucose
Components
  • Glucosidase 2 subunit beta
  • Neutral alpha-glucosidase AB
KeywordsHYDROLASE / Enzyme Glycosyl hydrolase GH31 Quality control exoglycosidase
Function / homology
Function and homology information


Glc2Man9GlcNAc2 oligosaccharide glucosidase activity / glucan 1,3-alpha-glucosidase activity / mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / nitrogen cycle metabolic process / 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 ...Glc2Man9GlcNAc2 oligosaccharide glucosidase activity / glucan 1,3-alpha-glucosidase activity / mannosyl-oligosaccharide alpha-1,3-glucosidase / glucosidase II complex / nitrogen cycle metabolic process / 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 / endoplasmic reticulum / Golgi apparatus / 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 / EF hand / : / Glycosyl hydrolase family 31 C-terminal domain / 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
FORMIC ACID / alpha-D-glucopyranose / OXAMIC ACID / D(-)-TARTARIC ACID / Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsCaputo, A.T. / Roversi, P. / Alonzi, D.S. / Kiappes, J.L. / Zitzmann, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structures of mammalian ER alpha-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals.
Authors: Caputo, A.T. / Alonzi, D.S. / Marti, L. / Reca, I.B. / Kiappes, J.L. / Struwe, W.B. / Cross, A. / Basu, S. / Lowe, E.D. / Darlot, B. / Santino, A. / Roversi, P. / Zitzmann, N.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)220,71355
Polymers214,9264
Non-polymers5,78751
Water7,764431
1
A: Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,52528
Polymers107,4632
Non-polymers3,06226
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)110,18827
Polymers107,4632
Non-polymers2,72525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.145, 170.741, 125.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 97894.625 Da / Num. of mol.: 2 / Fragment: UNP Residues 33-944
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q8BHN3, EC: 3.2.1.84
#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: 9568.298 Da / Num. of mol.: 2 / Fragment: UNP residues 30-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Plasmid: pHLsec / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: O08795

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Sugars , 2 types, 6 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 476 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: CH2O2
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#10: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#11: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 32 % Morpheus ethylene glycol/PEG 8000 mix, 0.05 M Morpheus carboxylic acids mix, 0.1 M Morpheus buffer system 1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.37→87.88 Å / Num. obs: 89708 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 33.37 Å2 / Rsym value: 0.24 / Net I/σ(I): 5.1
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 6578 / Rsym value: 1.53 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→87.66 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.882 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.414 / SU Rfree Blow DPI: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4422 4.95 %RANDOM
Rwork0.221 ---
obs0.223 89373 99.3 %-
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.8865 Å20 Å20 Å2
2---4.6399 Å20 Å2
3---6.5264 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.37→87.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15153 0 342 428 15923
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0130861HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.155477HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6621SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes380HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4586HARMONIC5
X-RAY DIFFRACTIONt_it30859HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.35
X-RAY DIFFRACTIONt_other_torsion14.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1973SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact34138SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.43 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 353 5.42 %
Rwork0.276 6159 -
all0.277 6512 -
obs--98.93 %

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