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

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Basic information

Entry
Database: PDB / ID: 6zdl
TitleStructure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG 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
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: 1.9 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 14, 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 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 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)50,2178
Polymers44,7831
Non-polymers5,4347
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint7 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.864, 127.864, 48.809
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 / 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


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, 119 molecules

#2: 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
#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-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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / 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: 0.97625 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→31.97 Å / Num. obs: 36208 / % possible obs: 100 % / Redundancy: 17.6 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.05 / Rrim(I) all: 0.209 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 17.4 % / Rmerge(I) obs: 3.43 / Mean I/σ(I) obs: 1 / Num. unique obs: 2322 / CC1/2: 0.546 / Rpim(I) all: 0.843 / Rrim(I) all: 3.534 / % possible all: 99.8

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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: 1.9→31.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.132
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2234 1779 4.917 %
Rwork0.1927 34405 -
all0.194 --
obs-36184 99.89 %
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: 29.729 Å2
Baniso -1Baniso -2Baniso -3
1--1.009 Å2-0.505 Å2-0 Å2
2---1.009 Å20 Å2
3---3.273 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 130 113 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133227
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172694
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.7774623
X-RAY DIFFRACTIONr_angle_other_deg2.4551.5836278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50622.012169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23315476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3611517
X-RAY DIFFRACTIONr_chiral_restr0.1330.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023455
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02696
X-RAY DIFFRACTIONr_nbd_refined0.1980.2606
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22616
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21526
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2149
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3480.211
X-RAY DIFFRACTIONr_nbd_other0.2780.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.29
X-RAY DIFFRACTIONr_mcbond_it1.4773.0351445
X-RAY DIFFRACTIONr_mcbond_other1.4763.0351446
X-RAY DIFFRACTIONr_mcangle_it2.2734.5461807
X-RAY DIFFRACTIONr_mcangle_other2.2734.5491808
X-RAY DIFFRACTIONr_scbond_it3.2383.5461782
X-RAY DIFFRACTIONr_scbond_other3.2383.5461782
X-RAY DIFFRACTIONr_scangle_it4.2835.5632739
X-RAY DIFFRACTIONr_scangle_other4.2835.5622740
X-RAY DIFFRACTIONr_lrange_it4.32135.243598
X-RAY DIFFRACTIONr_lrange_other4.29935.1513580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3241270.3342533X-RAY DIFFRACTION99.4393
1.949-2.0030.2831230.2962435X-RAY DIFFRACTION100
2.003-2.0610.3321300.2672402X-RAY DIFFRACTION100
2.061-2.1240.2661060.2522344X-RAY DIFFRACTION100
2.124-2.1940.2471190.2222231X-RAY DIFFRACTION100
2.194-2.2710.2721280.2142182X-RAY DIFFRACTION100
2.271-2.3560.223880.1962148X-RAY DIFFRACTION100
2.356-2.4530.2351180.182015X-RAY DIFFRACTION100
2.453-2.5620.2511060.181945X-RAY DIFFRACTION100
2.562-2.6870.223990.1851855X-RAY DIFFRACTION100
2.687-2.8320.2431130.1791758X-RAY DIFFRACTION100
2.832-3.0030.216780.181678X-RAY DIFFRACTION100
3.003-3.2110.211800.1851597X-RAY DIFFRACTION100
3.211-3.4680.201870.1831478X-RAY DIFFRACTION100
3.468-3.7980.192670.1851367X-RAY DIFFRACTION100
3.798-4.2460.206460.1771250X-RAY DIFFRACTION100
4.246-4.9020.183670.1611096X-RAY DIFFRACTION100
4.902-60.175370.175945X-RAY DIFFRACTION100
6-8.4730.238310.188739X-RAY DIFFRACTION100
8.473-31.970.23290.172407X-RAY DIFFRACTION97.9775

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