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- PDB-3u2u: Crystal Structure of Human Glycogenin-1 (GYG1) complexed with man... -

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Basic information

Entry
Database: PDB / ID: 3u2u
TitleCrystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and maltotetraose
ComponentsGlycogenin-1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / glycosyltransferase / glycogen biosynthesis / glycosylation / oligosaccharide / sugar chain / retaining anomeric configuration
Function / homology
Function and homology information


Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogenin glucosyltransferase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase activity / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis ...Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogenin glucosyltransferase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase activity / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis / lysosomal lumen / manganese ion binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / protein homodimerization activity / extracellular region / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / : / URIDINE-5'-DIPHOSPHATE / Glycogenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsChaikuad, A. / Froese, D.S. / Krysztofinska, E. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Yue, W.W. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.
Authors: Chaikuad, A. / Froese, D.S. / Berridge, G. / von Delft, F. / Oppermann, U. / Yue, W.W.
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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 2.2Nov 27, 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: Glycogenin-1
B: Glycogenin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,12315
Polymers59,2232
Non-polymers2,90013
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-54 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.765, 46.844, 69.848
Angle α, β, γ (deg.)79.36, 88.45, 77.20
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glycogenin-1 / GN-1 / GN1


Mass: 29611.639 Da / Num. of mol.: 2 / Fragment: glycogenin (residues 1-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYG, GYG1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P46976, glycogenin glucosyltransferase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(1+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 610 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.0M Ammonium Sulphate, 0.2M Na/K tartrate, 0.1M Na Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2010 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→45.6 Å / Num. all: 95225 / Num. obs: 95223 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.7
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.8 / Num. unique all: 13479 / % possible all: 91.6

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q4S

3q4s


Resolution: 1.45→41.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.214 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 4776 5 %RANDOM
Rwork0.16388 ---
obs0.16533 90447 94.52 %-
all-95223 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.031 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-1.04 Å20.27 Å2
2--0.2 Å20.68 Å2
3----1.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.164 Å
Refinement stepCycle: LAST / Resolution: 1.45→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 181 599 4929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224543
X-RAY DIFFRACTIONr_bond_other_d0.0010.022971
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9946210
X-RAY DIFFRACTIONr_angle_other_deg0.96737260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94924.043188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28815709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8561519
X-RAY DIFFRACTIONr_chiral_restr0.0950.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
X-RAY DIFFRACTIONr_mcbond_it2.31532673
X-RAY DIFFRACTIONr_mcbond_other0.67431062
X-RAY DIFFRACTIONr_mcangle_it3.71554363
X-RAY DIFFRACTIONr_scbond_it4.96281870
X-RAY DIFFRACTIONr_scangle_it7.058111833
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 322 -
Rwork0.262 6466 -
obs--91.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21340.2534-0.12970.3508-0.00440.8941-0.01570.0024-0.0113-0.01530.012-0.0046-0.0610.00830.00380.0414-0.0028-0.00390.02690.01030.036449.591927.555115.9062
20.16020.61920.05852.40280.2561.21490.01610.0056-0.02590.09590.0191-0.11770.2742-0.0156-0.03520.10680.0073-0.0070.0033-0.00420.044451.4027.305111.2196
30.33720.17760.05870.1228-0.0740.9952-0.0088-0.00110.01660.0118-0.0151-0.00130.0189-0.05820.0240.0377-0.00360.00630.0439-0.00350.038338.452318.564747.6108
41.5304-0.0285-0.14810.01960.20442.4825-0.02050.0774-0.0160.02190.01190.010.25910.40560.00860.03150.04940.00650.1252-0.01030.034157.921712.657253.0158
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 213
2X-RAY DIFFRACTION2A214 - 262
3X-RAY DIFFRACTION3B0 - 215
4X-RAY DIFFRACTION4B216 - 262

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