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

ID or keywords:

Entry

Database: PDB / ID: 4qlb

Title

Structural Basis for the Recruitment of Glycogen Synthase by Glycogenin

Components

Probable glycogen [starch] synthase
Protein GYG-1, isoform b

Keywords

TRANSFERASE / 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 / Neutrophil degranulation / glycogen(starch) synthase / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / glycogen biosynthetic process / glycosyltransferase activity ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Zeqiraj, E. / Judd, A. / Sicheri, F.

Citation

Journal: 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

Deposition	Jun 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 30, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4qlb.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4qlb.ent.gz	915.7 KB	Display	PDB format
PDBx/mmJSON format	4qlb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ql/4qlb ftp://data.pdbj.org/pub/pdb/validation_reports/ql/4qlb	HTTPS FTP

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Related structure data

Related structure data	3nazS 3nb0 S: Starting model for refinement
Similar structure data	4o9t-d 2nry-d 5f7k-d 5f7n-d 1ms8-d 2ajf-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

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

324 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by software
162 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by software
162 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1

#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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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.2 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2011 Details: Mirrors - Bent cylinders, Stripes of Pt, Rh and clear
Radiation	Monochromator: Cryo-Cooled double crystal - Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 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 % / B_iso Wilson estimate: 55.052 Å² / R_sym value: 0.115 / Net I/σ(I): 10.83
Reflection shell	Resolution: 2.6→2.67 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.51 / Num. unique all: 26837 / R_sym value: 1.244 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.9_1683)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NAZ

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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2241	2654	2.49 %	random
R_work	0.1791	-	-	-
all	0.1802	107023	-	-
obs	0.1802	106601	99.62 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.6→49.112 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21881	0	68	113	22062

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	22453
X-RAY DIFFRACTION	f_angle_d	0.576	30335
X-RAY DIFFRACTION	f_dihedral_angle_d	13.278	8331
X-RAY DIFFRACTION	f_chiral_restr	0.024	3243
X-RAY DIFFRACTION	f_plane_restr	0.002	3954

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6-2.6473	0.3482	141	0.3148	5275	X-RAY DIFFRACTION	97
2.6473-2.6982	0.3186	135	0.2761	5525	X-RAY DIFFRACTION	100
2.6982-2.7532	0.2915	120	0.2596	5425	X-RAY DIFFRACTION	100
2.7532-2.8131	0.3249	135	0.2586	5491	X-RAY DIFFRACTION	100
2.8131-2.8785	0.3432	136	0.2545	5482	X-RAY DIFFRACTION	100
2.8785-2.9505	0.2945	156	0.252	5467	X-RAY DIFFRACTION	100
2.9505-3.0303	0.3263	153	0.2476	5462	X-RAY DIFFRACTION	100
3.0303-3.1194	0.2996	159	0.2386	5466	X-RAY DIFFRACTION	100
3.1194-3.2201	0.2838	141	0.2206	5470	X-RAY DIFFRACTION	100
3.2201-3.3352	0.264	141	0.2033	5475	X-RAY DIFFRACTION	100
3.3352-3.4687	0.2691	132	0.1876	5475	X-RAY DIFFRACTION	100
3.4687-3.6265	0.2081	138	0.1703	5490	X-RAY DIFFRACTION	100
3.6265-3.8176	0.1797	125	0.1629	5490	X-RAY DIFFRACTION	100
3.8176-4.0567	0.1764	138	0.1487	5477	X-RAY DIFFRACTION	100
4.0567-4.3697	0.1884	138	0.134	5491	X-RAY DIFFRACTION	100
4.3697-4.8091	0.1568	138	0.1362	5514	X-RAY DIFFRACTION	100
4.8091-5.5042	0.1835	150	0.1441	5450	X-RAY DIFFRACTION	100
5.5042-6.9317	0.1902	129	0.1771	5512	X-RAY DIFFRACTION	99
6.9317-49.1211	0.206	149	0.1461	5510	X-RAY DIFFRACTION	98

Refinement TLS params.

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

ID	L11 (°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)
1	1.6055	-0.3741	0.1452	1.867	0.6433	2.0871	-0.0448	-0.1897	0.0689	0.1633	-0.0292	0.2984	-0.1706	-0.1942	0.0764	0.5295	0.0034	0.017	0.2548	0.024	0.4623	-0.0721	-1.7996	23.1401
2	0.9817	-1.279	0.8354	2.9511	-1.5439	1.0952	0.0426	-0.1229	-0.2619	-0.0858	0.113	0.63	0.0353	-0.1001	-0.1487	0.323	-0.0282	0.026	0.2378	-0.0268	0.4698	4.9153	-44.6579	10.4643
3	0.6311	0.1228	0.0109	2.8396	1.5404	0.9056	-0.0844	0.0017	0.092	0.0529	0.0293	0.1058	-0.2163	0.032	0.034	0.4501	-0.035	0.0034	0.2604	0.0103	0.3582	12.1312	-13.2359	9.266
4	0.6405	0.3057	0.9163	2.692	0.6578	1.5144	-0.1422	-0.0806	0.0642	-0.1481	-0.056	0.3209	-0.2865	-0.3827	0.2039	0.5649	0.0986	-0.0072	0.5137	0.0015	0.31	24.442	-42.1759	73.243
5	2.7528	-1.1233	1.7404	2.5252	-1.3295	2.8608	-0.1737	0.3663	0.5512	-0.2071	-0.0784	-0.2054	-0.5371	0.2081	0.2192	0.6766	-0.0628	0.0188	0.3707	0.0586	0.3482	44.7646	-29.6987	75.2627
6	1.3433	0.1361	0.4545	1.1292	0.3047	1.0406	0.0525	0.0269	-0.0291	-0.0289	-0.1106	-0.1	-0.163	-0.0634	0.0493	0.4784	0.0355	0.0346	0.3551	0.0549	0.2367	41.8553	-47.4754	79.4361
7	1.9284	-0.5838	-0.1189	1.6258	0.0275	3.5916	-0.005	0.2657	-0.2357	-0.054	0.0862	-0.011	0.1554	0.513	-0.0775	0.3651	-0.0098	0.0568	0.4432	-0.0667	0.3021	34.7328	-68.6619	46.4277
8	5.4401	-0.5192	4.2586	0.4082	-0.2839	4.5716	0.0337	0.2679	0.4803	-0.0263	-0.0857	-0.0577	-0.1625	0.7315	0.105	0.3817	-0.0973	0.0948	0.4669	0.0232	0.3792	27.3152	-58.9954	20.9133
9	1.3681	-0.7818	0.8984	0.4402	-0.5982	2.9464	0.1342	0.3741	0.0637	0.0112	-0.0079	-0.0398	0.1457	1.1137	-0.1188	0.4179	0.019	0.0792	0.6589	-0.0354	0.3816	38.973	-68.8781	32.4683
10	0.5962	0.2176	0.313	1.4003	1.4411	1.9638	-0.0882	0.0443	-0.097	0.2024	-0.0038	0.0603	0.022	-0.0837	0.0614	0.3932	0.0247	0.0579	0.3504	0.0328	0.2742	28.3261	-58.4704	65.0185
11	2.3751	0.2662	-0.4606	2.139	0.6718	3.084	0.0596	-0.0516	0.1507	0.0731	-0.1113	0.4479	0.0937	-0.4537	0.0271	0.271	-0.0571	0.0287	0.3158	0.0365	0.4991	-13.4935	-80.3424	28.8513
12	1.9934	1.1697	0.1102	1.627	-0.0435	0.2754	-0.2057	0.101	0.3624	-0.2149	0.0498	0.4192	-0.4592	-0.1183	0.1191	0.7185	0.071	-0.0425	0.4413	-0.0422	0.415	-3.215	-41.3689	45.7442
13	0.3421	-0.1634	0.1555	2.2338	2.2163	3.0378	-0.0609	-0.1904	-0.1142	0.3716	0.1058	0.1191	0.2651	-0.0255	-0.0197	0.3934	-0.0178	0.0699	0.3611	0.0361	0.4098	-4.0071	-74.7648	45.2462
14	0.5147	0.0623	-0.7641	2.7762	-0.0107	1.404	-0.0177	-0.1986	-0.044	0.0112	-0.0774	0.144	0.0621	0.1772	0.1194	0.2365	-0.0335	0.0222	0.5442	0.0376	0.3066	40.2852	-51.4884	-3.1412
15	3.2059	0.2088	-0.3599	0.7899	-0.039	0.6267	-0.0973	-0.6584	-0.5443	0.0175	-0.1168	-0.3367	0.4571	0.7048	0.1797	0.5164	0.1767	0.0893	0.8458	0.2697	0.54	54.8756	-69.7591	1.9848
16	1.8272	-0.1892	-0.3668	1.7509	-0.3556	0.8832	-0.0358	-0.6221	-0.0489	0.1048	-0.1503	-0.4274	-0.0315	0.9562	0.1088	0.3021	-0.0557	-0.0047	0.9434	0.1491	0.3699	59.3701	-52.04	-1.234
17	1.8045	-0.5411	-0.8921	0.2816	0.3323	2.0201	-0.1057	-0.3862	0.1508	0.2929	0.1326	-0.088	-0.1049	0.5797	-0.0249	0.8787	-0.1768	-0.1486	0.4992	0.0136	0.3776	41.1542	-28.632	35.8272
18	0.4043	-0.2902	-0.2563	1.7061	0.968	2.7711	-0.0922	0.0229	0.0796	0.1696	-0.0317	-0.1319	-0.2738	0.3774	0.0909	0.4056	-0.1728	-0.0511	0.4895	0.0613	0.33	44.9888	-36.5607	7.1742
19	9.544	1.1804	1.1955	6.2443	4.8722	3.8133	0.1978	-0.2553	0.7786	0.168	0.6536	-0.3845	-0.4038	0.4619	-0.7169	0.6192	-0.0478	-0.1048	0.358	0.0989	0.726	65.2113	-42.535	89.3917
20	5.6304	2.3001	-2.9117	7.9071	-5.1096	3.721	0.3631	-0.4412	-0.0022	0.3149	-0.1252	-0.5965	-0.2816	0.8724	-0.2608	0.4619	-0.0042	-0.0441	0.459	0.0462	0.3773	63.1831	-52.0171	86.8119
21	3.3661	-2.6263	-0.6127	3.3835	2.5107	3.2141	-0.3252	-1.2146	-0.5389	0.3314	0.5044	0.5886	-0.2371	-0.3168	-0.0793	0.484	-0.0386	-0.011	0.6244	0.1511	0.3761	50.2899	-48.7361	94.7334
22	3.6632	-1.9798	-1.942	1.6081	0.6705	7.0961	-0.0409	-0.5302	0.8145	0.2066	0.0384	1.5809	-1.4401	-0.4598	-0.0817	0.9178	0.2743	0.0423	0.8682	-0.144	1.384	-26.8151	9.0475	17.4486
23	2.0887	-1.9542	-1.0132	2.3531	-0.4733	5.7996	0.1899	0.303	0.0688	-0.3944	-0.041	1.3722	-0.6104	-1.4741	-0.1878	0.5387	0.2988	-0.3276	0.7262	-0.0409	1.3251	-24.4921	4.2006	8.7657
24	2.98	0.0819	1.8017	0.1445	0.7057	5.5289	-0.0711	0.0274	0.9114	-0.6362	-0.2972	1.1346	-1.4798	-0.3772	0.1308	0.8665	0.2144	-0.0292	0.4741	0.016	0.8893	-12.1985	13.6951	11.1314
25	4.6446	5.3907	0.1579	8.3984	1.0216	0.3892	-0.0138	0.1911	-0.0751	-0.7707	-0.4693	0.8909	0.31	-1.1865	0.4158	0.6471	-0.072	-0.0599	1.6834	-0.3145	0.9755	-41.9778	-82.0417	21.6531
26	2.707	0.2723	0.4905	0.1316	-0.1446	0.7445	-0.3183	0.5914	0.2143	-0.123	-0.131	0.3776	0.2372	-0.8276	0.0683	0.3229	-0.4139	0.2849	1.3178	-0.3291	1.1938	-37.411	-85.1158	32.643
27	1.9252	1.4644	1.6702	5.2214	-1.2811	3.0541	0.371	-0.0423	-0.1662	-0.4118	-0.222	-0.5416	0.4169	0.6048	0.0999	0.4518	0.0376	-0.0627	1.3334	0.3996	0.9581	82.1669	-60.0113	-0.2452
28	6.229	-0.8252	0.4205	5.208	3.5079	4.6187	0.158	0.2889	-0.2277	-0.3475	0.0232	-0.2726	-0.01	0.146	-0.3443	0.3471	0.2561	0.1345	1.3676	0.4621	0.7604	73.2639	-54.6433	-12.1036

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 310 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 311 through 525 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 526 through 654 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 6 through 84 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 85 through 162 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 163 through 310 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 311 through 398 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 399 through 432 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 433 through 498 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 499 through 654 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 7 through 310 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 311 through 542 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 543 through 664 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 5 through 84 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 85 through 162 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 163 through 310 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 311 through 498 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 499 through 653 )
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 268 through 278 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 279 through 289 )
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 290 through 301 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 268 through 278 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 279 through 289 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 290 through 301 )
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 269 through 278 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 279 through 301 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 268 through 289 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 290 through 302 )

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