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- PDB-1hxk: GOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH DEOXYMANNOJIRIMICIN -

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Basic information

Entry
Database: PDB / ID: 1hxk
TitleGOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH DEOXYMANNOJIRIMICIN
ComponentsALPHA-MANNOSIDASE II
KeywordsHYDROLASE / N-terminal alpha-beta domain / three helix bundle / 2 C-terminal beta barrels
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
Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / Immunoglobulin-like - #1360 / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 ...Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / Immunoglobulin-like - #1360 / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 / 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 families 57/38, central domain superfamily / Glycoside hydrolase 38, N-terminal 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
1-DEOXYMANNOJIRIMYCIN / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Authorsvan den Elsen, J.M.H. / Kuntz, D.A. / Rose, D.R.
CitationJournal: EMBO J. / Year: 2001
Title: Structure of Golgi alpha-mannosidase II: a target for inhibition of growth and metastasis of cancer cells.
Authors: van den Elsen, J.M. / Kuntz, D.A. / Rose, D.R.
History
DepositionJan 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_asym_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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-MANNOSIDASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7915
Polymers116,2231
Non-polymers5684
Water17,709983
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.814, 109.616, 138.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 II / GOLGI ALPHA-MANNOSIDASE II


Mass: 116222.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
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, 986 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DMJ / 1-DEOXYMANNOJIRIMYCIN


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4
#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.: 983 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, MPD, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18.5 %PEG60001reservoir
25 %MPD1reservoir
3100 mMTris1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 27, 2000
Details: bent cylindrical Si-mirror (Rh coating) bend cylindrical Ge(111) monochromator
RadiationMonochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→85.9 Å / Num. all: 158223 / Num. obs: 148337 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.6 Å2 / Limit h max: 42 / Limit h min: 0 / Limit k max: 66 / Limit k min: 0 / Limit l max: 87 / Limit l min: 0 / Observed criterion F max: 591889.39 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.3 / Num. unique all: 9246 / % possible all: 56
Reflection
*PLUS
Highest resolution: 1.69 Å / Num. obs: 114653 / % possible obs: 97.8 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 1.69 Å / Lowest resolution: 1.75 Å / % possible obs: 92.6 % / Rmerge(I) obs: 0.186

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HTY

1hty


Resolution: 1.5→85.9 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 6888 4.7 %RANDOM
Rwork0.197 ---
all-167398 --
obs-145650 87 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 40.8767 Å2 / ksol: 0.371343 e/Å3
Displacement parametersBiso max: 55.39 Å2 / Biso mean: 15.87 Å2 / Biso min: 3.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Luzzati d res high-1.5
Refinement stepCycle: LAST / Resolution: 1.5→85.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8181 0 34 983 9198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.19
X-RAY DIFFRACTIONc_improper_angle_d0.801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.5-1.570.2753641.80.256103410.013207501070551.6
1.57-1.650.2385362.60.224135680.01207421410468
1.65-1.750.2448103.90.212171230.007208411793386
1.75-1.890.2339794.70.202187740.006208101975394.9
1.89-2.080.21610104.80.196194150.006208902042597.8
2.08-2.380.21310354.90.194197240.006209422075999.1
2.38-30.21410685.10.196199030.006210582097199.6
3-85.90.204108650.186199140.006216012100097.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5cis_peptide.paramprotein.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.69 Å / Lowest resolution: 500 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.1969 / Rfactor Rfree: 0.2156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.19
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.801
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / % reflection Rfree: 1.8 % / Rfactor Rwork: 0.256

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