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- PDB-7kbr: Co-crystal structure of alpha glucosidase with compound 10 -

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Basic information

Entry
Database: PDB / ID: 7kbr
TitleCo-crystal structure of alpha glucosidase with compound 10
Components
  • (Neutral alpha-glucosidase AB Trypsin-cleaved Fragment ...) x 3
  • Glucosidase 2 subunit betaGlucosidases
KeywordsHYDROLASE / Alpha glucosidase II / Endoplasmic reticulum / Inhibitor complex
Function / homology
Function and homology information


mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development ...mannosyl-oligosaccharide alpha-1,3-glucosidase / glucan 1,3-alpha-glucosidase activity / glucosidase II complex / glucosidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / N-glycan processing / liver development / melanosome / negative regulation of neuron projection development / carbohydrate binding / in utero embryonic development / carbohydrate metabolic process / intracellular membrane-bounded organelle / calcium ion binding / protein-containing complex binding / Golgi apparatus / endoplasmic reticulum / RNA binding
Similarity search - Function
Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / MRH domain ...Glucosidase II beta subunit, N-terminal / Glucosidase II beta subunit-like / Glucosidase 2 subunit beta-like / Glucosidase II beta subunit-like / Glucosidase II beta subunit-like protein / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / MRH domain / MRH domain profile. / Mannose-6-phosphate receptor binding domain superfamily / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / EF hand / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Endoplasmic reticulum targeting sequence. / LDL receptor-like superfamily / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-WAS / Glucosidase 2 subunit beta / Neutral alpha-glucosidase AB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKarade, S.S. / Mariuzza, R.A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity.
Authors: Karade, S.S. / Hill, M.L. / Kiappes, J.L. / Manne, R. / Aakula, B. / Zitzmann, N. / Warfield, K.L. / Treston, A.M. / Mariuzza, R.A.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 5, 2022Group: 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 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
H: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
A: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
B: Glucosidase 2 subunit beta
I: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
J: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
C: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,83775
Polymers233,1868
Non-polymers6,65167
Water23,0771281
1
G: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
H: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
A: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
B: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,42042
Polymers116,5934
Non-polymers3,82738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1
J: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2
C: Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3
D: Glucosidase 2 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,41733
Polymers116,5934
Non-polymers2,82429
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.815, 102.815, 240.552
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 33 through 53 or (resid 54...
21(chain C and (resid 33 through 109 or (resid 110...
12(chain B and (resid 35 through 116 or (resid 117...
22(chain D and (resid 35 through 81 or (resid 82...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 33 through 53 or (resid 54...A33 - 53
121(chain A and (resid 33 through 53 or (resid 54...A54
131(chain A and (resid 33 through 53 or (resid 54...A33 - 966
141(chain A and (resid 33 through 53 or (resid 54...A33 - 966
151(chain A and (resid 33 through 53 or (resid 54...A33 - 966
161(chain A and (resid 33 through 53 or (resid 54...A33 - 966
211(chain C and (resid 33 through 109 or (resid 110...C33 - 109
221(chain C and (resid 33 through 109 or (resid 110...C110
231(chain C and (resid 33 through 109 or (resid 110...C33 - 966
241(chain C and (resid 33 through 109 or (resid 110...C33 - 966
251(chain C and (resid 33 through 109 or (resid 110...C33 - 966
261(chain C and (resid 33 through 109 or (resid 110...C33 - 966
112(chain B and (resid 35 through 116 or (resid 117...B35 - 116
122(chain B and (resid 35 through 116 or (resid 117...B117
132(chain B and (resid 35 through 116 or (resid 117...B35 - 117
142(chain B and (resid 35 through 116 or (resid 117...B35 - 117
152(chain B and (resid 35 through 116 or (resid 117...B35 - 117
162(chain B and (resid 35 through 116 or (resid 117...B35 - 117
212(chain D and (resid 35 through 81 or (resid 82...D35 - 81
222(chain D and (resid 35 through 81 or (resid 82...D82 - 83
232(chain D and (resid 35 through 81 or (resid 82...D34 - 117
242(chain D and (resid 35 through 81 or (resid 82...D34 - 117
252(chain D and (resid 35 through 81 or (resid 82...D34 - 117
262(chain D and (resid 35 through 81 or (resid 82...D34 - 117

NCS ensembles :
ID
1
2

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Components

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Neutral alpha-glucosidase AB Trypsin-cleaved Fragment ... , 3 types, 6 molecules GIHJAC

#1: Protein Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 20318.688 Da / Num. of mol.: 2 / Mutation: N97D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3, mannosyl-oligosaccharide alpha-1,3-glucosidase
#2: Protein Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 12052.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3, mannosyl-oligosaccharide alpha-1,3-glucosidase
#3: Protein Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3 / Alpha-glucosidase 2 / Glucosidase II subunit alpha


Mass: 69898.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ganab, G2an, Kiaa0088 / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8BHN3, mannosyl-oligosaccharide alpha-1,3-glucosidase

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Protein , 1 types, 2 molecules BD

#4: Protein Glucosidase 2 subunit beta / Glucosidases / 80K-H protein / Glucosidase II subunit beta / Protein kinase C substrate 60.1 kDa protein heavy chain / PKCSH


Mass: 14323.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prkcsh / Cell line (production host): Expi-HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08795

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Non-polymers , 8 types, 1348 molecules

#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-WAS / 2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethyl (2-{[(1S,2S,3R,4S,5S)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexyl]amino}ethyl)carbamate


Mass: 489.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H31N7O9 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1281 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09M NPS, 0.1M Buffer system 1 pH 7.0, 29%v/v P500MME_P20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2020 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.09→42.33 Å / Num. obs: 166814 / % possible obs: 99.52 % / Redundancy: 8.3 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1313 / Rpim(I) all: 0.048 / Rrim(I) all: 0.1399 / Net I/σ(I): 10.57
Reflection shellResolution: 2.09→2.169 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.9599 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 16182 / CC1/2: 0.683 / CC star: 0.901 / Rpim(I) all: 0.3796 / Rrim(I) all: 1.034 / % possible all: 97.06

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000v717.1data reduction
HKL-2000v717.1data scaling
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0E

5f0e


Resolution: 2.09→42.33 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 2022 1.21 %
Rwork0.1634 164537 -
obs0.1637 166559 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.84 Å2 / Biso mean: 37.3499 Å2 / Biso min: 12.1 Å2
Refinement stepCycle: final / Resolution: 2.09→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14913 0 423 1283 16619
Biso mean--56.98 43.44 -
Num. residues----1876
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8027X-RAY DIFFRACTION6.67TORSIONAL
12C8027X-RAY DIFFRACTION6.67TORSIONAL
21B712X-RAY DIFFRACTION6.67TORSIONAL
22D712X-RAY DIFFRACTION6.67TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.150.32541360.2711113021143896
2.15-2.20.29541420.23371173011872100
2.2-2.270.26031440.20951177611920100
2.27-2.340.23221460.20371190112047100
2.34-2.430.24521360.20551172511861100
2.43-2.520.24181380.18661185411992100
2.52-2.640.21071500.16921183511985100
2.64-2.780.20941440.18681181311957100
2.78-2.950.18641480.1771177411922100
2.95-3.180.18131500.15911181111961100
3.18-3.50.16521500.15451180111951100
3.5-40.16161460.14351182711973100
4-5.040.13971360.12131180311939100
5.04-42.330.16031560.1517115851174198

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