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Basic information

Entry
Database: PDB / ID: 5kk7
TitleCrystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase T688A mutant and Thio-disaccharide substrate analog complex
ComponentsEndoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
KeywordsHYDROLASE / alpha/alpha-barrel / cation replacement / protein-glycan interaction
Function / homology
Function and homology information


mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / protein glycosylation / ERAD pathway / ER Quality Control Compartment (ERQC) ...mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / protein glycosylation / ERAD pathway / ER Quality Control Compartment (ERQC) / trans-Golgi network / extracellular vesicle / cytoplasmic vesicle / Maturation of spike protein / viral protein processing / endosome / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / 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
methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / ACETATE ION / 1,4-BUTANEDIOL / Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7324 Å
AuthorsKaraveg, K. / Xiang, Y. / Moremen, K.W.
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 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / refine_hist / 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_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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.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 / _refine_hist.d_res_high / _struct_asym.entity_id
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: Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
B: Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,71020
Polymers104,5392
Non-polymers2,17118
Water21,4201189
1
A: Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,57511
Polymers52,2691
Non-polymers1,30510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1359
Polymers52,2691
Non-polymers8668
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.887, 56.302, 89.555
Angle α, β, γ (deg.)105.68, 94.15, 114.25
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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: 52269.359 Da / Num. of mol.: 2 / Mutation: T688A
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)-methyl 2-thio-alpha-D-mannopyranoside / methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 372.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a2-b1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp2SH]{[(2+S)][a-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 1205 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO3S
#6: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
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, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.732→42.16 Å / Num. obs: 85409 / % possible obs: 91 % / Redundancy: 1 % / Net I/σ(I): 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.7324→42.16 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 32.68
RfactorNum. reflection% reflection
Rfree0.2088 1983 2.33 %
Rwork0.1758 --
obs0.1766 85141 90.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7324→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7372 0 135 1189 8696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017966
X-RAY DIFFRACTIONf_angle_d1.06710808
X-RAY DIFFRACTIONf_dihedral_angle_d19.4154716
X-RAY DIFFRACTIONf_chiral_restr0.0571139
X-RAY DIFFRACTIONf_plane_restr0.0071391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7324-1.77570.3642740.27923416X-RAY DIFFRACTION52
1.7757-1.82380.25021210.26834618X-RAY DIFFRACTION71
1.8238-1.87740.27281280.24715440X-RAY DIFFRACTION83
1.8774-1.9380.31491500.23715932X-RAY DIFFRACTION91
1.938-2.00730.25541430.21726239X-RAY DIFFRACTION95
2.0073-2.08770.21661510.19976288X-RAY DIFFRACTION96
2.0877-2.18270.22591550.1886344X-RAY DIFFRACTION97
2.1827-2.29770.21721520.18576410X-RAY DIFFRACTION97
2.2977-2.44170.19521520.16826411X-RAY DIFFRACTION98
2.4417-2.63020.2071450.16546389X-RAY DIFFRACTION98
2.6302-2.89480.18611480.1596428X-RAY DIFFRACTION98
2.8948-3.31360.17581590.15396505X-RAY DIFFRACTION99
3.3136-4.17420.18821510.1326458X-RAY DIFFRACTION99
4.1742-42.40610.16381540.14126280X-RAY DIFFRACTION96
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)
10.4459-0.2230.16220.18860.07370.3720.0172-0.0154-0.0680.0071-0.00230.01220.07990.0216-0.00890.0942-0.0737-0.00310.18340.04040.039912.3619-8.58851.3474
22.68930.1076-0.31531.6049-0.47440.5706-0.0804-0.0691-0.46190.11790.00860.17470.088-0.00130.07650.1268-0.07230.00080.21850.01610.1456-7.0279-16.6662-0.094
30.70370.0277-0.11080.25480.01810.2732-0.00690.0529-0.04440.0023-0.02180.07240.04610.00210.0183-0.0226-0.02290.05780.1291-0.09090.0803-13.6756-5.3065-6.075
41.0557-0.47250.20331.26680.11550.6392-0.1084-0.12570.1730.0117-0.0034-0.0145-0.0233-0.02640.11830.12560.0208-0.01960.24250.03220.1757-0.717110.67512.2406
50.3825-0.09870.10450.3881-0.0240.21670.00620.0151-0.08970.04150.0128-0.06160.04230.02720.00630.09820.1287-0.00310.14920.0350.192438.6601-22.788544.7951
60.4976-0.0177-0.2350.38290.02440.2691-0.01650.0185-0.0727-0.02950.00170.00840.05010.00460.01570.0910.1407-0.00360.0513-0.01560.181622.1132-30.247438.4615
71.7725-1.45140.70982.3484-0.73320.5661-0.1619-0.3505-0.28110.2770.19720.11040.0496-0.0389-0.10580.15010.09490.01950.11990.02980.17111.6245-28.179848.0967
80.6316-0.1517-0.06180.6832-0.2440.8952-0.0265-0.0233-0.0758-0.0609-0.01810.1141-0.0029-0.095-0.07930.15710.0269-0.05130.17790.08320.161810.0215-20.053135.9997
90.14530.05550.05450.41380.16650.39410.00330.010.00180.0631-0.02330.0233-0.0891-0.0493-0.00760.05530.00990.00410.00330.0210.023414.9954-1.08942.941
100.3905-0.33770.03310.4774-0.03940.0967-0.0555-0.05070.03310.11860.0328-0.0156-0.05780.02280.00430.0966-0.0086-0.02390.02760.00090.036128.7168-1.88450.9611
110.79810.28430.51310.58190.38540.6113-0.05980.10510.0205-0.08070.03020.0113-0.06510.02520.00090.02490.0106-0.02740.0455-0.01510.02930.0895-13.29836.3474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 245 through 346 )
2X-RAY DIFFRACTION2chain 'A' and (resid 347 through 401 )
3X-RAY DIFFRACTION3chain 'A' and (resid 402 through 480 )
4X-RAY DIFFRACTION4chain 'A' and (resid 481 through 699 )
5X-RAY DIFFRACTION5chain 'B' and (resid 245 through 324 )
6X-RAY DIFFRACTION6chain 'B' and (resid 325 through 378 )
7X-RAY DIFFRACTION7chain 'B' and (resid 379 through 401 )
8X-RAY DIFFRACTION8chain 'B' and (resid 402 through 480 )
9X-RAY DIFFRACTION9chain 'B' and (resid 481 through 573 )
10X-RAY DIFFRACTION10chain 'B' and (resid 574 through 651 )
11X-RAY DIFFRACTION11chain 'B' and (resid 652 through 699 )

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