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- PDB-3blb: Crystal structure of Golgi Mannosidase II in complex with swainso... -

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Basic information

Entry
Database: PDB / ID: 3blb
TitleCrystal structure of Golgi Mannosidase II in complex with swainsonine at 1.3 Angstrom resolution
ComponentsAlpha-mannosidase 2
KeywordsHYDROLASE / Golgi mannosidase / Glycosidase / Golgi apparatus / Membrane / Signal-anchor / Transmembrane
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 / mannose metabolic process / N-glycan processing / 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 / mannose metabolic process / N-glycan processing / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / lysosome / Golgi membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Alpha-mannosidase 2, C-terminal sub-domain / : / Glycosyl hydrolases family 38 C-terminal sub-domain / Lysosomal alpha-mannosidase-like, central domain / Immunoglobulin-like - #1360 / 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 ...Alpha-mannosidase 2, C-terminal sub-domain / : / Glycosyl hydrolases family 38 C-terminal sub-domain / Lysosomal alpha-mannosidase-like, central domain / Immunoglobulin-like - #1360 / 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
1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKuntz, D.A. / Rose, D.R.
CitationJournal: To Be Published
Title: Golgi Mannosidase II in complex with swainsonine at 1.3 Angstrom.
Authors: Kuntz, D.A. / Rose, D.R.
History
DepositionDec 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
A: Alpha-mannosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2805
Polymers119,7021
Non-polymers5784
Water19,2401068
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.767, 109.662, 138.900
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 / Sugars , 2 types, 2 molecules A

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


Mass: 119701.617 Da / Num. of mol.: 1 / Fragment: Catalytic domain: Residues 76-1108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: Berkeley / Tissue: Head / Gene: alpha-Man-II, GmII, CG18802 / Plasmid: pMTBIP_NHIS / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells
References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1071 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SWA / 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL / SWAINSONINE


Mass: 173.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO3 / Comment: chemotherapy, inhibitor, alkaloid*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1068 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tris-HCl, PEG 6000, MPD, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.974 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 254722 / Num. obs: 254722 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.94 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.04
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.34 / Num. unique all: 13861 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HWW

1hww


Resolution: 1.3→29.83 Å / Rfactor Rfree error: 0.002 / FOM work R set: 0.9 / Data cutoff high absF: 261670.734 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.185 11766 4.8 %RANDOM
Rwork0.166 ---
all0.168 246212 --
obs0.168 246212 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.908 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å20 Å2
2--0.18 Å20 Å2
3---1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.12 Å
Luzzati d res low-30 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8181 0 35 1068 9284
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.95
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it3.042
X-RAY DIFFRACTIONc_scangle_it4.22.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.3-1.310.2852070.2636723879
1.31-1.320.2882070.25143414548
1.32-1.330.2412060.24143134519
1.33-1.340.2552080.2444164624
1.34-1.350.2432380.22543804618
1.35-1.360.2552170.23444294646
1.36-1.370.2522220.22344324654
1.37-1.380.2322320.2244704702
1.38-1.390.2692290.20744714700
1.39-1.40.2142180.20544554673
1.4-1.410.2122400.20145104750
1.41-1.420.2122290.19845734802
1.42-1.440.2122390.19245604799
1.44-1.450.1882310.18845184749
1.45-1.460.2292380.1945854823
1.46-1.480.2062630.17745534816
1.48-1.490.2042380.17546514889
1.49-1.510.2072260.17246084834
1.51-1.520.2042340.17446484882
1.52-1.540.2042560.1746514907
1.54-1.560.2012390.16746604899
1.56-1.580.1962420.16246804922
1.58-1.60.1922590.15747004959
1.6-1.620.1861380.15447584896
1.62-1.640.1691440.15348544998
1.64-1.660.1891620.15447364898
1.66-1.680.1772130.15147694982
1.68-1.710.1891880.15447744962
1.71-1.740.162090.14647314940
1.74-1.760.1652140.14447975011
1.76-1.790.1742230.14647684991
1.79-1.830.1712540.14747835037
1.83-1.860.1812530.1547715024
1.86-1.90.172560.14848015057
1.9-1.940.1662490.14847595008
1.94-1.990.1652530.15448355088
1.99-2.040.1672610.15348295090
2.04-2.090.1962370.15648845121
2.09-2.150.1672760.15248715147
2.15-2.220.1762410.15748885129
2.22-2.30.1772630.14948635126
2.3-2.390.1892670.1548795146
2.39-2.50.1642870.15148675154
2.5-2.640.182570.15549195176
2.64-2.80.1762560.15949155171
2.8-3.020.1872420.1649725214
3.02-3.320.1642630.15449695232
3.32-3.80.1562890.14249665255
3.8-4.780.1433070.13950045311
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3cis_peptide.paramcis_peptide.top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top
X-RAY DIFFRACTION5ion.paramion.top

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