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- PDB-3t7n: Crystal Structure of Human Glycogenin-1 (GYG1) complexed with man... -

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Basic information

Entry
Database: PDB / ID: 3t7n
TitleCrystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP, in a monoclinic closed form
ComponentsGlycogenin-1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / glycosyltransferase / glycogen biosynthesis / glycosylation
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 / cytoplasm / cytosol
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
: / URIDINE-5'-DIPHOSPHATE / Glycogenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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
DepositionJul 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)60,1416
Polymers59,2232
Non-polymers9184
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-58 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.020, 80.720, 69.850
Angle α, β, γ (deg.)90.00, 100.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29611.639 Da / Num. of mol.: 2 / Fragment: glycogenin (UNP 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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.2M MgCl2, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 19, 2011
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→30.43 Å / Num. all: 34716 / Num. obs: 34694 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.7
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4921 / % possible all: 95.3

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Processing

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

3q4s


Resolution: 1.98→29.16 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.519 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26546 1745 5 %RANDOM
Rwork0.20326 ---
obs0.20632 32947 96.99 %-
all-34694 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å2-2.48 Å2
2--2.61 Å20 Å2
3----2.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 1.98→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 0 52 286 4365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224236
X-RAY DIFFRACTIONr_bond_other_d0.0010.022735
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9615786
X-RAY DIFFRACTIONr_angle_other_deg0.97436690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52124.185184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1515655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.511517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
X-RAY DIFFRACTIONr_mcbond_it0.7011.52573
X-RAY DIFFRACTIONr_mcbond_other0.171.51024
X-RAY DIFFRACTIONr_mcangle_it1.23424187
X-RAY DIFFRACTIONr_scbond_it1.94731663
X-RAY DIFFRACTIONr_scangle_it2.7724.51593
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 132 -
Rwork0.303 2356 -
obs--94.64 %
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)
12.46581.0992-0.52382.24421.44441.92310.0073-0.21110.0484-0.05420.03260.0015-0.0342-0.0458-0.03990.0324-0.0255-0.03470.23480.01170.042430.90495.550767.8038
20.92520.46690.13920.2735-0.09771.36430.00410.0717-0.0402-0.03040.03240.01520.00770.1498-0.03650.0923-0.0141-0.03160.05750.01560.089536.4060.484153.0194
32.078-0.5144-0.03461.01590.77480.74780.11850.18130.0274-0.1994-0.08610.008-0.0983-0.1348-0.03230.114-0.0218-0.06550.12920.03850.055814.61593.839553.9147
444.80628.8311-12.129418.5582-7.8023.2861-2.23633.3135-0.2574-1.48382.1459-0.20440.5826-0.9150.09040.57120.04940.09890.37050.0920.24249.066710.288953.0554
57.0833-0.96670.86520.7825-2.63899.88070.001-0.55-0.35610.0150.09770.0677-0.0647-0.1772-0.09870.005-0.0121-0.02640.14410.10880.17415.03655.437768.0428
61.86220.21840.79960.6778-0.20721.66940.0730.1230.0125-0.07220.03490.04210.1392-0.0058-0.10790.099-0.0042-0.02050.0984-0.02220.029318.4242-3.793614.0378
77.449-2.201-0.12953.4319-1.07212.5385-0.0232-0.69240.12320.19440.2530.22060.2923-0.0763-0.22980.1357-0.0146-0.03020.0807-0.01780.071715.7548-10.296623.8334
81.68280.33780.2220.4444-0.42611.53460.1049-0.0712-0.06190.0315-0.0304-0.08830.17230.0429-0.07450.10080.012-0.05310.0591-0.02780.074423.153-9.803630.725
92.83712.2063-2.54372.62431.281415.8781-0.1475-0.13920.2269-0.1268-0.23980.3634-0.62670.22060.38740.2437-0.1345-0.03760.1394-0.05650.099429.6649.20334.5878
104.9930.81660.97365.4169-3.1812.3225-0.0342-0.33610.60441.02980.05680.295-0.7265-0.1388-0.02260.41610.02120.05320.03990.00740.213419.059413.325519.1781
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 80
2X-RAY DIFFRACTION2A81 - 188
3X-RAY DIFFRACTION3A189 - 230
4X-RAY DIFFRACTION4A231 - 243
5X-RAY DIFFRACTION5A244 - 262
6X-RAY DIFFRACTION6B1 - 68
7X-RAY DIFFRACTION7B69 - 100
8X-RAY DIFFRACTION8B101 - 188
9X-RAY DIFFRACTION9B189 - 211
10X-RAY DIFFRACTION10B212 - 262

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