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- PDB-5iee: Murine endoplasmic reticulum alpha-glucosidase II with 1-deoxynoj... -

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Basic information

Entry
Database: PDB / ID: 5iee
TitleMurine endoplasmic reticulum alpha-glucosidase II with 1-deoxynojirimycin
Components
  • Glucosidase 2 subunit beta
  • Neutral alpha-glucosidase AB
KeywordsHYDROLASE / Enzyme Glycosyl hydrolase GH31 Quality control exoglycosidase / DNJ
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 / 1-DEOXYNOJIRIMYCIN / Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsCaputo, A.T. / Roversi, P. / Alonzi, D.S. / Kiappes, J.L. / Zitzmann, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust097300/Z/11/Z United Kingdom
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
DepositionFeb 25, 2016Deposition 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.type

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,93829
Polymers115,7262
Non-polymers3,21227
Water17,114950
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint36 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.480, 173.710, 62.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 106157.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-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.: 1
Source method: isolated from a genetically manipulated source
Details: This chain contains all of the residues from the mature O08795 but has been trypsinised so that there all that was crystallised are residues: 30-117
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Plasmid: pOPING / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: O08795

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Type: D-saccharide / Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4

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Non-polymers , 6 types, 975 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H18O5
Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84 / Comment: precipitant*YM
#5: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C12H26O7
Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84 / Comment: precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: CH2O2
Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence ...Details: This chain contains all of the residues from the mature Q8BHN3 isoform 2 (i.e. no signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ganab / Plasmid: pOPINGS / Cell (production host): ENDOTHELIAL / Cell line (production host): HEK 293-F / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: EC: 3.2.1.84
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21% v/v ethylene glycol, 11% w/v PEG 8000 (from the Morpheus Precipitant Mix 2), 50 mM Morpheus carboxylic acids mix, 100 mM Morpheus buffer system 1 pH 6.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.919→88.901 Å / Num. obs: 87597 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.34 Å2 / Rsym value: 0.239 / Net I/σ(I): 7.2
Reflection shellResolution: 1.919→1.925 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROCdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5F0E

5f0e


Resolution: 1.92→88.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.196 4312 4.94 %RANDOM
Rwork0.164 ---
obs0.166 87327 99.9 %-
Displacement parametersBiso mean: 28.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.2677 Å20 Å20 Å2
2---1.0136 Å20 Å2
3---0.7459 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.92→88.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7577 0 196 950 8723
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115623HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0728069HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3354SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes190HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2322HARMONIC5
X-RAY DIFFRACTIONt_it15623HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.35
X-RAY DIFFRACTIONt_other_torsion14.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion987SEMIHARMONIC5
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_contact17694SEMIHARMONIC4
LS refinement shellHighest resolution: 1.92 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.257 341 5.38 %
Rwork0.233 6001 -
obs--99.7 %

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