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- PDB-6zj5: Structure of the catalytic domain of human endo-alpha-mannosidase... -

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Basic information

Entry
Database: PDB / ID: 6zj5
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcDMJ 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
1-DEOXYMANNOJIRIMYCIN / alpha-D-glucopyranose / 6-tungstotellurate(VI) / Glycoprotein endo-alpha-1,2-mannosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.269 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 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 2.0Jan 20, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_related_exp_data_set / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Jan 31, 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)50,71010
Polymers44,7831
Non-polymers5,9269
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint18 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.549, 128.549, 48.264
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11AAA-637-

HOH

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Components

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Protein / Sugars , 2 types, 2 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
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / 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, 102 molecules

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


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 1614.626 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: O24TeW6
#5: Chemical ChemComp-DMJ / 1-DEOXYMANNOJIRIMYCIN


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.57 Å3/Da / Density % sol: 52.2 % / Description: hexagonal, flat
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 7.5 - 8.1, 200 mM MgCl2, 25-27.5% v/v PEG 400, 1 mM TEW Protein in 25 mM HEPES pH 7.0, 200 mM NaCl buffer at 10 mg/ml.
PH range: 7.5-8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.269→111.327 Å / Num. obs: 11089 / % possible obs: 51.9 % / Redundancy: 8 % / CC1/2: 0.989 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.103 / Rrim(I) all: 0.295 / Net I/σ(I): 5.3
Reflection shellResolution: 2.269→2.536 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.52 / Num. unique obs: 925 / CC1/2: 0.569 / Rpim(I) all: 0.547 / Rrim(I) all: 1.617 / % possible all: 15.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
STARANISO1.0.4data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZFA

6zfa


Resolution: 2.269→111.327 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.174 / SU B: 10.303 / SU ML: 0.246 / Average fsc free: 0.8681 / Average fsc work: 0.8925 / Cross valid method: FREE R-VALUE / ESU R Free: 0.408
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2559 545 4.915 %
Rwork0.1882 10544 -
all0.192 --
obs-11089 51.903 %
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: 29.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.579 Å20.289 Å20 Å2
2--0.579 Å2-0 Å2
3----1.878 Å2
Refinement stepCycle: LAST / Resolution: 2.269→111.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 161 94 3248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133288
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172819
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.7794697
X-RAY DIFFRACTIONr_angle_other_deg1.1261.5866516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6065361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65922.045176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51215483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7341518
X-RAY DIFFRACTIONr_chiral_restr0.0590.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02776
X-RAY DIFFRACTIONr_nbd_refined0.2070.2759
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22890
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21514
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21420
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.220
X-RAY DIFFRACTIONr_nbd_other0.2540.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3380.26
X-RAY DIFFRACTIONr_mcbond_it1.7742.9821447
X-RAY DIFFRACTIONr_mcbond_other1.7682.9771446
X-RAY DIFFRACTIONr_mcangle_it2.9284.4621807
X-RAY DIFFRACTIONr_mcangle_other2.9284.4691808
X-RAY DIFFRACTIONr_scbond_it2.4743.5881841
X-RAY DIFFRACTIONr_scbond_other2.4743.5881841
X-RAY DIFFRACTIONr_scangle_it3.1765.6972818
X-RAY DIFFRACTIONr_scangle_other3.1755.6962819
X-RAY DIFFRACTIONr_lrange_it6.66335.273755
X-RAY DIFFRACTIONr_lrange_other6.65635.2783740
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 work% reflection obs (%)WRfactor RworkFsc free
2.269-2.32800.3460.315790.8682.91320.302
2.328-2.3920.463100.2851490.29415120.82310.51590.280.61
2.392-2.4610.45460.2932970.29714780.81920.50070.2860.817
2.461-2.5370.343260.2973910.314430.80428.89810.2820.747
2.537-2.620.485230.2694720.27913980.79935.40770.2580.753
2.62-2.7120.333170.2725310.27413480.77540.65280.2580.781
2.712-2.8150.353450.2795820.28413210.80747.4640.2550.744
2.815-2.9290.341290.2646230.26712470.83952.28550.2380.821
2.929-3.060.4340.2236760.2312170.86658.34020.1980.797
3.06-3.2090.266350.2177020.2211730.88262.83030.1930.905
3.209-3.3820.223510.1986690.210770.91166.85240.1720.916
3.382-3.5870.209440.1837520.18510560.92475.37880.160.927
3.587-3.8350.308310.1747590.1799730.93481.19220.1560.887
3.835-4.1410.258260.1587750.1619330.94685.85210.1470.925
4.141-4.5360.269420.1466730.1528340.95585.73140.1360.92
4.536-5.070.193390.1636680.1657800.94790.6410.1480.951
5.07-5.8530.229280.1716070.1746830.93792.97220.1590.92
5.853-7.1630.223180.1775320.1795840.93794.17810.170.916
7.163-10.1090.209240.1614090.1644600.9694.13040.1730.943
10.109-111.3270.191170.1712300.1722680.96892.16420.1960.965

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