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- PDB-6rry: GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymeth... -

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Basic information

Entry
Database: PDB / ID: 6rry
TitleGOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-1,2,3,6-tetrahydro-3-pyridinol
ComponentsAlpha-mannosidase 2
KeywordsHYDROLASE / Mannosidase / Glycoside Hydrolase
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack / protein glycosylation / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Immunoglobulin-like - #1360 / Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Golgi alpha-mannosidase II; domain 4 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel ...Immunoglobulin-like - #1360 / Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Golgi alpha-mannosidase II; domain 4 / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / Alpha-Beta Barrel / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-KGE / SUCCINIC ACID / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsArmstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M. / Geurink, P.P. ...Armstrong, Z. / Lahav, D. / Johnson, R. / Kuo, C.L. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M. / Geurink, P.P. / Ovaa, H. / van der Stelt, M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / Davies, G.J.
Funding support United Kingdom, Netherlands, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R001162/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
European Research CouncilERC-2011-AdG-290836 Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.
Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / ...Authors: Armstrong, Z. / Kuo, C.L. / Lahav, D. / Liu, B. / Johnson, R. / Beenakker, T.J.M. / de Boer, C. / Wong, C.S. / van Rijssel, E.R. / Debets, M.F. / Florea, B.I. / Hissink, C. / Boot, R.G. / Geurink, P.P. / Ovaa, H. / van der Stelt, M. / van der Marel, G.M. / Codee, J.D.C. / Aerts, J.M.F.G. / Wu, L. / Overkleeft, H.S. / Davies, G.J.
History
DepositionMay 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-mannosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7077
Polymers118,2081
Non-polymers4996
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint16 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.473, 90.366, 132.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-mannosidase 2 / Golgi alpha-mannosidase II / Man II / Golgi alpha-mannosidase IIa / Mannosyl-oligosaccharide 1 / 3- ...Golgi alpha-mannosidase II / Man II / Golgi alpha-mannosidase IIa / Mannosyl-oligosaccharide 1 / 3-1 / 6-alpha-mannosidase


Mass: 118208.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-IIa, GmII, CG18802 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Hi Five
References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase

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Non-polymers , 5 types, 496 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-KGE / (2~{S},3~{R})-2-(hydroxymethyl)-1,2,3,6-tetrahydropyridin-3-ol


Mass: 129.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium succinate, pH 7.4 10 % PEG 3350 with microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.86→90.37 Å / Num. obs: 91011 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.996 / Net I/σ(I): 12.4
Reflection shellResolution: 1.86→1.89 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4451 / CC1/2: 0.705 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bub

3bub


Resolution: 1.86→74.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 4527 5 %RANDOM
Rwork0.1859 ---
obs0.1881 86399 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.11 Å2 / Biso mean: 34.862 Å2 / Biso min: 18.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å2-0 Å20 Å2
2--2.32 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 1.86→74.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8065 0 30 490 8585
Biso mean--43.33 38.49 -
Num. residues----1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138407
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177569
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.64411421
X-RAY DIFFRACTIONr_angle_other_deg2.3471.57217595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41351015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55421.983469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98151401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6351556
X-RAY DIFFRACTIONr_chiral_restr0.0760.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029411
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021833
X-RAY DIFFRACTIONr_mcbond_it2.8143.6114030
X-RAY DIFFRACTIONr_mcbond_other2.8123.6114029
X-RAY DIFFRACTIONr_mcangle_it3.855.45040
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 347 -
Rwork0.309 6298 -
all-6645 -
obs--99.88 %

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