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- PDB-5hjr: Murine endoplasmic reticulum alpha-glucosidase II with bound cova... -

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Basic information

Entry
Database: PDB / ID: 5hjr
TitleMurine endoplasmic reticulum alpha-glucosidase II with bound covalent intermediate
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
5-fluoro-beta-D-glucopyranose / FORMIC ACID / 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 / Resolution: 2.4 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
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)219,28459
Polymers213,6154
Non-polymers5,67055
Water7,638424
1
A: Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,60730
Polymers106,8072
Non-polymers2,79928
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)109,67829
Polymers106,8072
Non-polymers2,87127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.512, 174.664, 63.714
Angle α, β, γ (deg.)90.00, 91.31, 90.00
Int Tables number4
Space group name H-MP1211

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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 34-966
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 / 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: 8912.645 Da / Num. of mol.: 2 / Fragment: UNP residues 35-117
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 , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-5GF / 5-fluoro-beta-D-glucopyranose / 5-fluoro-beta-D-glucose / 5-fluoro-D-glucose / 5-fluoro-glucose


Type: D-saccharide, beta linking / Mass: 198.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H11FO6

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Non-polymers , 7 types, 475 molecules

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


Mass: 62.068 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C2H6O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Plasmid: pHLsec / Cell line (production host): HEK293-F / Production host: Homo sapiens (human)
#6: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Formula: CH2O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Plasmid: pHLsec / Cell line (production host): HEK293-F / Production host: Homo sapiens (human)
#8: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3NO3
#10: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#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.: 424 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
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: I03 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.4→174.66 Å / Num. obs: 87472 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 56.53 Å2 / Rsym value: 0.246 / Net I/σ(I): 7.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.364 / Rsym value: 2.526 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.4→103.48 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.325 / SU Rfree Blow DPI: 0.201
RfactorNum. reflection% reflectionSelection details
Rfree0.202 4409 5.06 %RANDOM
Rwork0.177 ---
obs0.179 87211 98.9 %-
Displacement parametersBiso mean: 59.28 Å2
Baniso -1Baniso -2Baniso -3
1-8.7516 Å20 Å2-4.0433 Å2
2---14.3793 Å20 Å2
3---5.6277 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→103.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15017 0 341 424 15782
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0130520HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1354745HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6483SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes370HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4572HARMONIC5
X-RAY DIFFRACTIONt_it30518HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.31
X-RAY DIFFRACTIONt_other_torsion15.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1966SEMIHARMONIC5
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_contact32525SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.284 328 5.16 %
Rwork0.232 6024 -
obs--97 %

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