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- PDB-4qlb: Structural Basis for the Recruitment of Glycogen Synthase by Glyc... -

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Basic information

Entry
Database: PDB / ID: 4qlb
TitleStructural Basis for the Recruitment of Glycogen Synthase by Glycogenin
Components
  • Probable glycogen [starch] synthase
  • Protein GYG-1, isoform b
KeywordsTRANSFERASE / protein-protein complex / glycosyltransferase / GT-B fold / Rossmann fold domain / glycogen synthesis / glycogenin
Function / homology
Function and homology information


Glycogen synthesis / Glycogen breakdown (glycogenolysis) / striated muscle dense body / glycogen(starch) synthase / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / glycogen (starch) synthase activity / glycogen biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Glycogen synthase / Glycogen synthase / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Glycogen Phosphorylase B; / Nucleotide-diphospho-sugar transferases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycogenin-1 / Glycogenin-1 / Glycogen [starch] synthase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZeqiraj, E. / Judd, A. / Sicheri, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the recruitment of glycogen synthase by glycogenin.
Authors: Zeqiraj, E. / Tang, X. / Hunter, R.W. / Garcia-Rocha, M. / Judd, A. / Deak, M. / von Wilamowitz-Moellendorff, A. / Kurinov, I. / Guinovart, J.J. / Tyers, M. / Sakamoto, K. / Sicheri, F.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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 / _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: Probable glycogen [starch] synthase
C: Probable glycogen [starch] synthase
D: Probable glycogen [starch] synthase
B: Probable glycogen [starch] synthase
G: Protein GYG-1, isoform b
E: Protein GYG-1, isoform b
H: Protein GYG-1, isoform b
F: Protein GYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,46821
Polymers323,2318
Non-polymers1,23713
Water2,036113
1
A: Probable glycogen [starch] synthase
C: Probable glycogen [starch] synthase
G: Protein GYG-1, isoform b
E: Protein GYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,28011
Polymers161,6154
Non-polymers6657
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-137 kcal/mol
Surface area54490 Å2
MethodPISA
2
D: Probable glycogen [starch] synthase
B: Probable glycogen [starch] synthase
H: Protein GYG-1, isoform b
F: Protein GYG-1, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,18810
Polymers161,6154
Non-polymers5726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-138 kcal/mol
Surface area55670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.590, 162.880, 115.790
Angle α, β, γ (deg.)90.00, 95.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable glycogen [starch] synthase


Mass: 76691.227 Da / Num. of mol.: 4 / Fragment: glycogen synthase / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gsy-1, Y46G5A.31 / Plasmid: pProEx-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9U2D9, glycogen(starch) synthase
#2: Protein/peptide
Protein GYG-1, isoform b


Mass: 4116.446 Da / Num. of mol.: 4 / Fragment: glycogenin (residues 268-302) / Mutation: none / Source method: obtained synthetically
Details: This sequence of gyg-1 (amino acids 268-302) occurs naturally in C. elegans
Source: (synth.) Caenorhabditis elegans (invertebrata) / References: UniProt: Q95Q50, UniProt: H2KYQ5*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: 100 mM bis-Tris propane (pH 7.25), 200 mM NaSO4 and 22% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2011
Details: Mirrors - Bent cylinders, Stripes of Pt, Rh and clear
RadiationMonochromator: Cryo-Cooled double crystal - Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 106616 / % possible obs: 99.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.8 % / Biso Wilson estimate: 55.052 Å2 / Rsym value: 0.115 / Net I/σ(I): 10.83
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.51 / Num. unique all: 26837 / Rsym value: 1.244 / % possible all: 97.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1683)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NAZ
Resolution: 2.6→49.112 Å / SU ML: 0.35 / Isotropic thermal model: isotropic + TLS / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 2654 2.49 %random
Rwork0.1791 ---
all0.1802 107023 --
obs0.1802 106601 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→49.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21881 0 68 113 22062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222453
X-RAY DIFFRACTIONf_angle_d0.57630335
X-RAY DIFFRACTIONf_dihedral_angle_d13.2788331
X-RAY DIFFRACTIONf_chiral_restr0.0243243
X-RAY DIFFRACTIONf_plane_restr0.0023954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64730.34821410.31485275X-RAY DIFFRACTION97
2.6473-2.69820.31861350.27615525X-RAY DIFFRACTION100
2.6982-2.75320.29151200.25965425X-RAY DIFFRACTION100
2.7532-2.81310.32491350.25865491X-RAY DIFFRACTION100
2.8131-2.87850.34321360.25455482X-RAY DIFFRACTION100
2.8785-2.95050.29451560.2525467X-RAY DIFFRACTION100
2.9505-3.03030.32631530.24765462X-RAY DIFFRACTION100
3.0303-3.11940.29961590.23865466X-RAY DIFFRACTION100
3.1194-3.22010.28381410.22065470X-RAY DIFFRACTION100
3.2201-3.33520.2641410.20335475X-RAY DIFFRACTION100
3.3352-3.46870.26911320.18765475X-RAY DIFFRACTION100
3.4687-3.62650.20811380.17035490X-RAY DIFFRACTION100
3.6265-3.81760.17971250.16295490X-RAY DIFFRACTION100
3.8176-4.05670.17641380.14875477X-RAY DIFFRACTION100
4.0567-4.36970.18841380.1345491X-RAY DIFFRACTION100
4.3697-4.80910.15681380.13625514X-RAY DIFFRACTION100
4.8091-5.50420.18351500.14415450X-RAY DIFFRACTION100
5.5042-6.93170.19021290.17715512X-RAY DIFFRACTION99
6.9317-49.12110.2061490.14615510X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6055-0.37410.14521.8670.64332.0871-0.0448-0.18970.06890.1633-0.02920.2984-0.1706-0.19420.07640.52950.00340.0170.25480.0240.4623-0.0721-1.799623.1401
20.9817-1.2790.83542.9511-1.54391.09520.0426-0.1229-0.2619-0.08580.1130.630.0353-0.1001-0.14870.323-0.02820.0260.2378-0.02680.46984.9153-44.657910.4643
30.63110.12280.01092.83961.54040.9056-0.08440.00170.0920.05290.02930.1058-0.21630.0320.0340.4501-0.0350.00340.26040.01030.358212.1312-13.23599.266
40.64050.30570.91632.6920.65781.5144-0.1422-0.08060.0642-0.1481-0.0560.3209-0.2865-0.38270.20390.56490.0986-0.00720.51370.00150.3124.442-42.175973.243
52.7528-1.12331.74042.5252-1.32952.8608-0.17370.36630.5512-0.2071-0.0784-0.2054-0.53710.20810.21920.6766-0.06280.01880.37070.05860.348244.7646-29.698775.2627
61.34330.13610.45451.12920.30471.04060.05250.0269-0.0291-0.0289-0.1106-0.1-0.163-0.06340.04930.47840.03550.03460.35510.05490.236741.8553-47.475479.4361
71.9284-0.5838-0.11891.62580.02753.5916-0.0050.2657-0.2357-0.0540.0862-0.0110.15540.513-0.07750.3651-0.00980.05680.4432-0.06670.302134.7328-68.661946.4277
85.4401-0.51924.25860.4082-0.28394.57160.03370.26790.4803-0.0263-0.0857-0.0577-0.16250.73150.1050.3817-0.09730.09480.46690.02320.379227.3152-58.995420.9133
91.3681-0.78180.89840.4402-0.59822.94640.13420.37410.06370.0112-0.0079-0.03980.14571.1137-0.11880.41790.0190.07920.6589-0.03540.381638.973-68.878132.4683
100.59620.21760.3131.40031.44111.9638-0.08820.0443-0.0970.2024-0.00380.06030.022-0.08370.06140.39320.02470.05790.35040.03280.274228.3261-58.470465.0185
112.37510.2662-0.46062.1390.67183.0840.0596-0.05160.15070.0731-0.11130.44790.0937-0.45370.02710.271-0.05710.02870.31580.03650.4991-13.4935-80.342428.8513
121.99341.16970.11021.627-0.04350.2754-0.20570.1010.3624-0.21490.04980.4192-0.4592-0.11830.11910.71850.071-0.04250.4413-0.04220.415-3.215-41.368945.7442
130.3421-0.16340.15552.23382.21633.0378-0.0609-0.1904-0.11420.37160.10580.11910.2651-0.0255-0.01970.3934-0.01780.06990.36110.03610.4098-4.0071-74.764845.2462
140.51470.0623-0.76412.7762-0.01071.404-0.0177-0.1986-0.0440.0112-0.07740.1440.06210.17720.11940.2365-0.03350.02220.54420.03760.306640.2852-51.4884-3.1412
153.20590.2088-0.35990.7899-0.0390.6267-0.0973-0.6584-0.54430.0175-0.1168-0.33670.45710.70480.17970.51640.17670.08930.84580.26970.5454.8756-69.75911.9848
161.8272-0.1892-0.36681.7509-0.35560.8832-0.0358-0.6221-0.04890.1048-0.1503-0.4274-0.03150.95620.10880.3021-0.0557-0.00470.94340.14910.369959.3701-52.04-1.234
171.8045-0.5411-0.89210.28160.33232.0201-0.1057-0.38620.15080.29290.1326-0.088-0.10490.5797-0.02490.8787-0.1768-0.14860.49920.01360.377641.1542-28.63235.8272
180.4043-0.2902-0.25631.70610.9682.7711-0.09220.02290.07960.1696-0.0317-0.1319-0.27380.37740.09090.4056-0.1728-0.05110.48950.06130.3344.9888-36.56077.1742
199.5441.18041.19556.24434.87223.81330.1978-0.25530.77860.1680.6536-0.3845-0.40380.4619-0.71690.6192-0.0478-0.10480.3580.09890.72665.2113-42.53589.3917
205.63042.3001-2.91177.9071-5.10963.7210.3631-0.4412-0.00220.3149-0.1252-0.5965-0.28160.8724-0.26080.4619-0.0042-0.04410.4590.04620.377363.1831-52.017186.8119
213.3661-2.6263-0.61273.38352.51073.2141-0.3252-1.2146-0.53890.33140.50440.5886-0.2371-0.3168-0.07930.484-0.0386-0.0110.62440.15110.376150.2899-48.736194.7334
223.6632-1.9798-1.9421.60810.67057.0961-0.0409-0.53020.81450.20660.03841.5809-1.4401-0.4598-0.08170.91780.27430.04230.8682-0.1441.384-26.81519.047517.4486
232.0887-1.9542-1.01322.3531-0.47335.79960.18990.3030.0688-0.3944-0.0411.3722-0.6104-1.4741-0.18780.53870.2988-0.32760.7262-0.04091.3251-24.49214.20068.7657
242.980.08191.80170.14450.70575.5289-0.07110.02740.9114-0.6362-0.29721.1346-1.4798-0.37720.13080.86650.2144-0.02920.47410.0160.8893-12.198513.695111.1314
254.64465.39070.15798.39841.02160.3892-0.01380.1911-0.0751-0.7707-0.46930.89090.31-1.18650.41580.6471-0.072-0.05991.6834-0.31450.9755-41.9778-82.041721.6531
262.7070.27230.49050.1316-0.14460.7445-0.31830.59140.2143-0.123-0.1310.37760.2372-0.82760.06830.3229-0.41390.28491.3178-0.32911.1938-37.411-85.115832.643
271.92521.46441.67025.2214-1.28113.05410.371-0.0423-0.1662-0.4118-0.222-0.54160.41690.60480.09990.45180.0376-0.06271.33340.39960.958182.1669-60.0113-0.2452
286.229-0.82520.42055.2083.50794.61870.1580.2889-0.2277-0.34750.0232-0.2726-0.010.146-0.34430.34710.25610.13451.36760.46210.760473.2639-54.6433-12.1036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 310 )
2X-RAY DIFFRACTION2chain 'A' and (resid 311 through 525 )
3X-RAY DIFFRACTION3chain 'A' and (resid 526 through 654 )
4X-RAY DIFFRACTION4chain 'C' and (resid 6 through 84 )
5X-RAY DIFFRACTION5chain 'C' and (resid 85 through 162 )
6X-RAY DIFFRACTION6chain 'C' and (resid 163 through 310 )
7X-RAY DIFFRACTION7chain 'C' and (resid 311 through 398 )
8X-RAY DIFFRACTION8chain 'C' and (resid 399 through 432 )
9X-RAY DIFFRACTION9chain 'C' and (resid 433 through 498 )
10X-RAY DIFFRACTION10chain 'C' and (resid 499 through 654 )
11X-RAY DIFFRACTION11chain 'D' and (resid 7 through 310 )
12X-RAY DIFFRACTION12chain 'D' and (resid 311 through 542 )
13X-RAY DIFFRACTION13chain 'D' and (resid 543 through 664 )
14X-RAY DIFFRACTION14chain 'B' and (resid 5 through 84 )
15X-RAY DIFFRACTION15chain 'B' and (resid 85 through 162 )
16X-RAY DIFFRACTION16chain 'B' and (resid 163 through 310 )
17X-RAY DIFFRACTION17chain 'B' and (resid 311 through 498 )
18X-RAY DIFFRACTION18chain 'B' and (resid 499 through 653 )
19X-RAY DIFFRACTION19chain 'G' and (resid 268 through 278 )
20X-RAY DIFFRACTION20chain 'G' and (resid 279 through 289 )
21X-RAY DIFFRACTION21chain 'G' and (resid 290 through 301 )
22X-RAY DIFFRACTION22chain 'E' and (resid 268 through 278 )
23X-RAY DIFFRACTION23chain 'E' and (resid 279 through 289 )
24X-RAY DIFFRACTION24chain 'E' and (resid 290 through 301 )
25X-RAY DIFFRACTION25chain 'H' and (resid 269 through 278 )
26X-RAY DIFFRACTION26chain 'H' and (resid 279 through 301 )
27X-RAY DIFFRACTION27chain 'F' and (resid 268 through 289 )
28X-RAY DIFFRACTION28chain 'F' and (resid 290 through 302 )

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