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- PDB-5mhf: Murine endoplasmic reticulum alpha-glucosidase I with N-9'-methox... -

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Basic information

Entry
Database: PDB / ID: 5mhf
TitleMurine endoplasmic reticulum alpha-glucosidase I with N-9'-methoxynonyl-1-deoxynojirimycin.
ComponentsMannosyl-oligosaccharide glucosidase
KeywordsHYDROLASE / GH63 / Glucosidase / Iminosugar
Function / homology
Function and homology information


mannosyl-oligosaccharide glucosidase / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation / endoplasmic reticulum membrane
Similarity search - Function
Glycosyl hydrolase family 63, C-terminal / Glycosyl hydrolase family 63, N-terminal / Glycosyl hydrolase family 63, N-terminal domain superfamily / Glycosyl hydrolase family 63 C-terminal domain / Glycosyl hydrolase family 63 N-terminal domain / Glycoside hydrolase family 63 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
N-9'-methoxynonyl-1-deoxynojirimycin / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / Mannosyl-oligosaccharide glucosidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHill, J.C. / Caputo, A.T. / Roversi, P. / Zitzmann, N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust106272/Z/14/Z United Kingdom
Wellcome Trust097300/Z/11/Z United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: Targeting Endoplasmic Reticulum alpha-Glucosidase I with a Single-Dose Iminosugar Treatment Protects against Lethal Influenza and Dengue Virus Infections.
Authors: Warfield, K.L. / Alonzi, D.S. / Hill, J.C. / Caputo, A.T. / Roversi, P. / Kiappes, J.L. / Sheets, N. / Duchars, M. / Dwek, R.A. / Biggins, J. / Barnard, D. / Shresta, S. / Treston, A.M. / Zitzmann, N.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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 2.2Apr 24, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mannosyl-oligosaccharide glucosidase
B: Mannosyl-oligosaccharide glucosidase
C: Mannosyl-oligosaccharide glucosidase
D: Mannosyl-oligosaccharide glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,04230
Polymers355,2834
Non-polymers6,75926
Water24,9871387
1
A: Mannosyl-oligosaccharide glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2377
Polymers88,8211
Non-polymers1,4166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mannosyl-oligosaccharide glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2377
Polymers88,8211
Non-polymers1,4166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mannosyl-oligosaccharide glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7848
Polymers88,8211
Non-polymers1,9637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mannosyl-oligosaccharide glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7848
Polymers88,8211
Non-polymers1,9637
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.010, 130.920, 135.370
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Mannosyl-oligosaccharide glucosidase / Glucosidase 1 / Glycoprotein-processing glucosidase I


Mass: 88820.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mogs, Gcs1 / Plasmid: pOPINGS / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: Q80UM7, mannosyl-oligosaccharide glucosidase

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Sugars , 2 types, 4 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1409 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-6A9 / N-9'-methoxynonyl-1-deoxynojirimycin


Mass: 319.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H33NO5
#6: Chemical
ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H36O9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1387 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.09M Morpheus NPS, 0.1M Morpheus Buffer System 1 pH 6.5, 50% v/v Morpheus Precipitant Mix 1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.1→133.5 Å / Num. obs: 215063 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.107 Å / Redundancy: 3 % / Rmerge(I) obs: 1.164 / Mean I/σ(I) obs: 1 / CC1/2: 0.482 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J5T

4j5t


Resolution: 2.1→133.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.216 10477 4.88 %RANDOM
Rwork0.188 ---
obs0.189 214780 99.4 %-
Displacement parametersBiso mean: 43.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.7734 Å20 Å2-0.4281 Å2
2--3.471 Å20 Å2
3----1.6976 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.1→133.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23398 0 1052 1387 25837
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125555HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0834820HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8308SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes496HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3684HARMONIC5
X-RAY DIFFRACTIONt_it25555HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion17.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3025SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact26961SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 784 4.97 %
Rwork0.22 14997 -
all0.221 15781 -
obs--98.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1790.0855-0.09530.702-0.41530.8806-0.00160.07690.17040.00710.06470.099-0.08280.0039-0.0631-0.2218-0.0327-0.02490.13740.0413-0.180348.8118.314.2273
21.18190.20390.310.67860.41190.9294-0.0616-0.09250.16240.04060.026-0.0197-0.0348-0.1090.0357-0.24750.0623-0.04010.1991-0.0346-0.215216.73418.0569-49.0017
30.6763-0.0016-0.06080.13820.18762.4589-0.05830.01610.0080.0510.0418-0.05790.14010.19590.0166-0.22590.0364-0.0180.1848-0.0078-0.230258.81071.2138-52.457
40.99770.0732-0.23130.162-0.05721.4354-0.04490.1714-0.0105-0.03690.01220.04540.083-0.18520.0327-0.2287-0.0398-0.01380.2239-0.0068-0.21576.83581.038717.4527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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