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- PDB-5hjo: Murine endoplasmic reticulum alpha-glucosidase II with bound subs... -

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Basic information

Entry
Database: PDB / ID: 5hjo
TitleMurine endoplasmic reticulum alpha-glucosidase II with bound substrate analogue
Components
  • Glucosidase 2 subunit betaGlucosidases
  • Neutral alpha-glucosidase AB
KeywordsHYDROLASE / Enzyme Glycosyl hydrolase / GH31 / Quality control exoglycosidase
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. / MRH domain ...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. / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / 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
ACETATE ION / D-glucal / FORMIC ACID / Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.29 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / 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 / software / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_src_gen.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _software.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)217,31238
Polymers213,6154
Non-polymers3,69734
Water11,674648
1
A: Neutral alpha-glucosidase AB
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,65619
Polymers106,8072
Non-polymers1,84917
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)108,65619
Polymers106,8072
Non-polymers1,84917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.050, 176.440, 103.480
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 / Glucosidases / 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, 6 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.: 2
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 2-deoxy-alpha-D-arabino-hexopyranose-(1-3)-D-glucal


Type: oligosaccharide / Mass: 292.282 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[zz122h_1-5][ad122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1,2-deoxy-Glcp]{[(3+1)][a-D-2-deoxy-Glcp]{}}LINUCSPDB-CARE
#8: Sugar ChemComp-DGO / D-glucal / Glucal


Type: D-saccharide / Mass: 146.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O4

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Non-polymers , 5 types, 676 molecules

#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H3O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: GANAB / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human)
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: GANAB / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human)
#7: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Formula: CH2O2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: GANAB / Plasmid: pHLsec / Cell line (production host): HEK293-F / Organ (production host): Kidney / Production host: Homo sapiens (human)
#9: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 30 % Morpheus ethylene glycol/PEG 8000 mix, 0.1 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: I02 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.29→103.1 Å / Num. obs: 101815 / % possible obs: 96.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 44.1 Å2 / Rsym value: 0.206 / Net I/σ(I): 8.7
Reflection shellResolution: 2.29→2.297 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.1 / Num. measured obs: 3622 / Num. unique all: 731 / CC1/2: 0.552 / Rsym value: 1.484 / % possible all: 70.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.29→103.1 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.87 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.214
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5023 4.95 %RANDOM
Rwork0.204 ---
obs0.206 101524 96.6 %-
Displacement parametersBiso mean: 46.79 Å2
Baniso -1Baniso -2Baniso -3
1-10.5388 Å20 Å20 Å2
2---24.3694 Å20 Å2
3---13.8306 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.29→103.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15010 0 240 648 15898
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0130272HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.154344HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6427SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes373HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4536HARMONIC5
X-RAY DIFFRACTIONt_it30270HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.4
X-RAY DIFFRACTIONt_other_torsion14.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1969SEMIHARMONIC5
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_contact32929SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.35 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.283 311 5.56 %
Rwork0.253 5284 -
obs--72.7 %

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