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- PDB-5clt: Crystal structure of human glycogen branching enzyme (GBE1) in co... -

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Basic information

Entry
Database: PDB / ID: 5clt
TitleCrystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose
Components1,4-alpha-glucan-branching enzyme
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Glycogen storage disease type IV (GBE1) / cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / glycogen metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycogen synthesis / generation of precursor metabolites and energy ...Glycogen storage disease type IV (GBE1) / cation binding / 1,4-alpha-glucan branching enzyme / : / 1,4-alpha-glucan branching enzyme activity / glycogen biosynthetic process / glycogen metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycogen synthesis / generation of precursor metabolites and energy / carbohydrate binding / negative regulation of neuron apoptotic process / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...1,4-alpha-glucan-branching enzyme / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-acarbose / 1,4-alpha-glucan-branching enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsKrojer, T. / Froese, D.S. / Goubin, S. / Strain-Damerell, C. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. ...Krojer, T. / Froese, D.S. / Goubin, S. / Strain-Damerell, C. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Yue, W. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose
Authors: Krojer, T. / Froese, D.S. / Goubin, S. / Strain-Damerell, C. / Mahajan, P. / Burgess-Brown, N. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Yue, W. / Structural Genomics Consortium (SGC)
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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: 1,4-alpha-glucan-branching enzyme
B: 1,4-alpha-glucan-branching enzyme
C: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,0476
Polymers231,1103
Non-polymers1,9373
Water00
1
A: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6822
Polymers77,0371
Non-polymers6461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6822
Polymers77,0371
Non-polymers6461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1,4-alpha-glucan-branching enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6822
Polymers77,0371
Non-polymers6461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.760, 163.990, 311.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA44 - 1000
211chain BB43 - 1000
311chain CC45 - 1000

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Components

#1: Protein 1,4-alpha-glucan-branching enzyme / Brancher enzyme / Glycogen-branching enzyme


Mass: 77036.742 Da / Num. of mol.: 3 / Fragment: residues 38-700
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBE1 / Plasmid: pFB-LIC-Bse / Production host: unidentified baculovirus
References: UniProt: Q04446, 1,4-alpha-glucan branching enzyme
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE

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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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium formate , 3% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.79→72.56 Å / Num. obs: 74282 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 48.86 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.069 / Net I/σ(I): 10 / Num. measured all: 279440
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.79-2.863.80.6972.12083554240.6920.40299.7
12.48-72.563.50.03929.231388910.9960.02397.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZY

4bzy


Resolution: 2.79→58.38 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 3741 5.04 %
Rwork0.1937 70520 -
obs0.196 74261 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.52 Å2 / Biso mean: 39.0292 Å2 / Biso min: 9.83 Å2
Refinement stepCycle: final / Resolution: 2.79→58.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15324 0 261 0 15585
Biso mean--55.94 --
Num. residues----1920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915939
X-RAY DIFFRACTIONf_angle_d1.25321648
X-RAY DIFFRACTIONf_chiral_restr0.0522227
X-RAY DIFFRACTIONf_plane_restr0.0072792
X-RAY DIFFRACTIONf_dihedral_angle_d13.7715638
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8946X-RAY DIFFRACTION5.413TORSIONAL
12B8946X-RAY DIFFRACTION5.413TORSIONAL
13C8946X-RAY DIFFRACTION5.413TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.82540.34791280.273625642692100
2.8254-2.86250.34611530.26862578273199
2.8625-2.90180.31381480.259325582706100
2.9018-2.94320.31681260.243426292755100
2.9432-2.98710.3081350.242525782713100
2.9871-3.03380.28871500.251726122762100
3.0338-3.08350.30941240.243525922716100
3.0835-3.13670.29931370.247126052742100
3.1367-3.19370.31221300.233825532683100
3.1937-3.25520.29131450.231326282773100
3.2552-3.32160.28271480.232625732721100
3.3216-3.39380.2631430.22882585272899
3.3938-3.47280.31631240.231526272751100
3.4728-3.55960.28581320.218125982730100
3.5596-3.65580.22881270.21942600272799
3.6558-3.76340.26641580.20412577273599
3.7634-3.88480.24171220.192326372759100
3.8848-4.02360.26191250.181226432768100
4.0236-4.18470.19541390.168425982737100
4.1847-4.37510.1851480.143226012749100
4.3751-4.60570.17641390.151326392778100
4.6057-4.89410.17181280.145726302758100
4.8941-5.27180.19991630.149426232786100
5.2718-5.80180.17771400.16362631277199
5.8018-6.64040.23021480.175126512799100
6.6404-8.36220.21891430.18212685282899
8.3622-58.39280.20511380.17712725286398

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