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Basic information

Entry
Database: PDB / ID: 5kij
TitleCrystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex
ComponentsEndoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
KeywordsHYDROLASE / alpha/alpha-barrel / cation replacement / protein-glycan interaction
Function / homology
Function and homology information


: / protein alpha-1,2-demannosylation / Defective MAN1B1 causes MRT15 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / oligosaccharide metabolic process / endoplasmic reticulum quality control compartment / : / ERAD pathway ...: / protein alpha-1,2-demannosylation / Defective MAN1B1 causes MRT15 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / oligosaccharide metabolic process / endoplasmic reticulum quality control compartment / : / ERAD pathway / ER Quality Control Compartment (ERQC) / extracellular vesicle / cytoplasmic vesicle / Maturation of spike protein / viral protein processing / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / membrane
Similarity search - Function
: / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1,4-BUTANEDIOL / LANTHANUM (III) ION / Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å
AuthorsKaraveg, K. / Xiang, Y. / Moremen, K.W.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM047533 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK075322 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103390 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM107012 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.
Authors: Xiang, Y. / Karaveg, K. / Moremen, K.W.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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 / struct_asym / struct_conn / struct_conn_type / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_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_ptnr2_label_alt_id / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,44110
Polymers52,0301
Non-polymers2,4119
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint20 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.625, 53.830, 56.118
Angle α, β, γ (deg.)89.65, 63.60, 62.70
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase / ER alpha-1 / 2-mannosidase / ER mannosidase 1 / ERMan1 / Man9GlcNAc2-specific-processing alpha- ...ER alpha-1 / 2-mannosidase / ER mannosidase 1 / ERMan1 / Man9GlcNAc2-specific-processing alpha-mannosidase / Mannosidase alpha class 1B member 1


Mass: 52030.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAN1B1, UNQ747/PRO1477 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q9UKM7, mannosyl-oligosaccharide 1,2-alpha-mannosidase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1518.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3-3-3-3-3-3/a4-b1_b3-c1_b6-e1_c2-d1_e3-f1_e6-h1_f2-g1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 613 molecules

#3: Chemical ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: La
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H11NO3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG 4000, 50mM ammonium sulfate, 0.1M MES, 10% 1,4-butanediol, pH 6.5, 200mM NDSB-200, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.649→48.69 Å / Num. obs: 53113 / % possible obs: 96.5 % / Redundancy: 1.9 % / Net I/σ(I): 9
Reflection shellResolution: 1.649→1.691 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X9D

1x9d


Resolution: 1.649→27.081 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 2.03 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1996 3.76 %
Rwork0.1825 --
obs0.1841 53095 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.649→27.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 0 150 605 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064066
X-RAY DIFFRACTIONf_angle_d0.8845529
X-RAY DIFFRACTIONf_dihedral_angle_d12.4862426
X-RAY DIFFRACTIONf_chiral_restr0.051605
X-RAY DIFFRACTIONf_plane_restr0.006691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6493-1.69060.23881460.193447X-RAY DIFFRACTION92
1.6906-1.73630.24541290.18463569X-RAY DIFFRACTION94
1.7363-1.78740.23371380.18343560X-RAY DIFFRACTION95
1.7874-1.84510.21771350.17893670X-RAY DIFFRACTION96
1.8451-1.9110.24541400.1713606X-RAY DIFFRACTION96
1.911-1.98750.21371320.18183673X-RAY DIFFRACTION96
1.9875-2.07790.18631450.18233666X-RAY DIFFRACTION97
2.0779-2.18740.23471500.17873635X-RAY DIFFRACTION97
2.1874-2.32440.26181380.18053688X-RAY DIFFRACTION97
2.3244-2.50370.2371360.19413698X-RAY DIFFRACTION98
2.5037-2.75550.22831510.19593700X-RAY DIFFRACTION98
2.7555-3.15370.23121480.19373727X-RAY DIFFRACTION98
3.1537-3.97130.20921510.17153721X-RAY DIFFRACTION99
3.9713-27.08490.19471570.17633739X-RAY DIFFRACTION99

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