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- PDB-6zfa: Structure of the catalytic domain of human endo-alpha-mannosidase... -

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Basic information

Entry
Database: PDB / ID: 6zfa
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG, alpha-1,2-mannobiose and hexatungstotellurate(VI) TEW
ComponentsGlycoprotein endo-alpha-1,2-mannosidase
KeywordsHYDROLASE / Golgi / mannosidase / retaining
Function / homology
Function and homology information


glycoprotein endo-alpha-1,2-mannosidase / glycoprotein endo-alpha-1,2-mannosidase activity / N-glycan trimming and elongation in the cis-Golgi / alpha-mannosidase activity / Golgi membrane / Golgi apparatus
Similarity search - Function
Glycosyl hydrolase family 99 / Glycosyl hydrolase family 99 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
2alpha-alpha-mannobiose / alpha-D-glucopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / 6-tungstotellurate(VI) / Glycoprotein endo-alpha-1,2-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. ...Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J.
Funding support United Kingdom, Australia, 4items
OrganizationGrant numberCountry
European Research Council (ERC)322942 United Kingdom
Australian Research Council (ARC)DP120101396 Australia
Australian Research Council (ARC)FT130100103 Australia
Australian Research Council (ARC)DP180101957 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.
Authors: Sobala, L.F. / Fernandes, P.Z. / Hakki, Z. / Thompson, A.J. / Howe, J.D. / Hill, M. / Zitzmann, N. / Davies, S. / Stamataki, Z. / Butters, T.D. / Alonzi, D.S. / Williams, S.J. / Davies, G.J.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 20, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Glycoprotein endo-alpha-1,2-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5599
Polymers44,7831
Non-polymers5,7768
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint17 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.891, 127.891, 48.352
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Glycoprotein endo-alpha-1,2-mannosidase / hEndo / Mandaselin


Mass: 44783.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MANEA / Plasmid: pCold-I / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5SRI9, glycoprotein endo-alpha-1,2-mannosidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 142 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O24TeW6
#6: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: hexagonal
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM MgCl2, 30% v/v PEG 400 (Alfa Aesar), 1 mM Anderson-Evans polyoxotungstate TEW. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.8→110.76 Å / Num. obs: 42149 / % possible obs: 100 % / Redundancy: 16.5 % / Biso Wilson estimate: 21.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.038 / Rrim(I) all: 0.153 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.939 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2447 / CC1/2: 0.782 / Rpim(I) all: 0.237 / Rrim(I) all: 0.969 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALS1.8.4-g04a6c08a-releasedata reduction
Aimless0.6.2data scaling
REFMAC5.8.0189phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZDK

6zdk


Resolution: 1.8→110.757 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2166 2094 4.973 %
Rwork0.1855 40010 -
all0.187 --
obs-42104 99.936 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.893 Å2-0.447 Å2-0 Å2
2---0.893 Å20 Å2
3---2.898 Å2
Refinement stepCycle: LAST / Resolution: 1.8→110.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 153 136 3231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133278
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172749
X-RAY DIFFRACTIONr_angle_refined_deg2.2151.7914696
X-RAY DIFFRACTIONr_angle_other_deg2.7321.5966425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.8345.577390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83222.012164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76715476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1421516
X-RAY DIFFRACTIONr_chiral_restr0.1370.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023929
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02702
X-RAY DIFFRACTIONr_nbd_refined0.1970.2611
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.22595
X-RAY DIFFRACTIONr_nbtor_refined0.180.21536
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2170
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3560.214
X-RAY DIFFRACTIONr_nbd_other0.2680.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.29
X-RAY DIFFRACTIONr_mcbond_it1.5192.421445
X-RAY DIFFRACTIONr_mcbond_other1.5182.421446
X-RAY DIFFRACTIONr_mcangle_it2.2913.6241808
X-RAY DIFFRACTIONr_mcangle_other2.2913.6261809
X-RAY DIFFRACTIONr_scbond_it3.092.8871833
X-RAY DIFFRACTIONr_scbond_other3.092.8871833
X-RAY DIFFRACTIONr_scangle_it4.064.5012809
X-RAY DIFFRACTIONr_scangle_other4.0594.52810
X-RAY DIFFRACTIONr_lrange_it5.03628.3023637
X-RAY DIFFRACTIONr_lrange_other5.01828.1813613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3441560.32529050.32630670.6650.68799.80440.315
1.847-1.8970.2951650.2828540.28130190.7760.7911000.265
1.897-1.9520.2671370.26127850.26129220.8410.8491000.244
1.952-2.0120.241530.23427190.23428720.8720.8871000.217
2.012-2.0780.2681320.21126090.21427410.8740.8981000.194
2.078-2.1510.2441240.19925450.20126690.8980.9161000.18
2.151-2.2330.2691330.19224490.19625820.9040.921000.174
2.233-2.3240.2391110.18123950.18325060.9270.9431000.164
2.324-2.4270.2131250.17122580.17423830.9350.9451000.156
2.427-2.5450.2441190.1721840.17423030.9240.9481000.155
2.545-2.6830.1741090.15720620.15821710.9580.9611000.143
2.683-2.8460.2291270.16519340.16920610.9350.9561000.154
2.846-3.0420.235820.16718520.1719340.9360.9541000.158
3.042-3.2850.156830.17217160.17117990.9690.9591000.165
3.285-3.5990.197930.1715760.17216690.9610.9591000.166
3.599-4.0230.205640.17514590.17615230.9540.9581000.173
4.023-4.6440.191540.15612710.15713250.970.9691000.156
4.644-5.6850.167600.17210860.17211460.9680.9631000.173
5.685-8.030.236350.198690.1929040.9420.9551000.19
8.03-110.7570.185320.184820.185140.9620.9681000.192

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