PDB-5vnc: Glycogen synthase in complex with UDP and glucosamine

ID or keywords:

Entry

Database: PDB / ID: 5vnc

Title

Glycogen synthase in complex with UDP and glucosamine

Components

Glycogen [starch] synthase isoform 2

Keywords

TRANSFERASE / Glycogen synthase / UDP-glucosamine / glucosamine / complex / glucosyl transfer

Function / homology

Function and homology information

Glycogen synthesis / glycogen binding / glycogen(starch) synthase / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / glycogen granule / glycogen biosynthetic process / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.98 Å

Authors

Mahalingan, K.K. / Hurley, T.D.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Glycogen synthase in complex with UDP and glucosamine
Authors: Mahalingan, K.K. / Hurley, T.D.

History

Deposition	Apr 30, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 2, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.d_res_low Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2	Mar 23, 2022	Group: Author supporting evidence / Database references / Structure summary Category: chem_comp / database_2 / pdbx_audit_support Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3	Oct 4, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vnc.cif.gz	1000.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5vnc.ent.gz	838 KB	Display	PDB format
PDBx/mmJSON format	5vnc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5vnc_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	5vnc_full_validation.pdf.gz	2.7 MB	Display
Data in XML	5vnc_validation.xml.gz	83.1 KB	Display
Data in CIF	5vnc_validation.cif.gz	112.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vn/5vnc ftp://data.pdbj.org/pub/pdb/validation_reports/vn/5vnc	HTTPS FTP

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Related structure data

Related structure data	3nb0S S: Starting model for refinement
Similar structure data	5uw0-d 5uw4-d 5uw1-d 3nb0-d 3rt1-d 5ux7-d 4kq1-d 4kq2-d 5suk-d 4kqm-d 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) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Glycogen [starch] synthase isoform 2

B: Glycogen [starch] synthase isoform 2

C: Glycogen [starch] synthase isoform 2

D: Glycogen [starch] synthase isoform 2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	193.044, 204.698, 205.888
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D

NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	GLU	GLU	A	A	2 - 16	22 - 36
2	1	1	SER	SER	GLU	GLU	B	B	2 - 16	22 - 36
3	1	1	SER	SER	GLU	GLU	C	C	2 - 16	22 - 36
4	1	1	SER	SER	GLU	GLU	D	D	2 - 16	22 - 36
1	2	1	ARG	ARG	ASN	ASN	A	A	20 - 50	40 - 70
2	2	1	ARG	ARG	ASN	ASN	B	B	20 - 50	40 - 70
3	2	1	ARG	ARG	ASN	ASN	C	C	20 - 50	40 - 70
4	2	1	ARG	ARG	ASN	ASN	D	D	20 - 50	40 - 70
1	3	1	MET	MET	LEU	LEU	A	A	73 - 125	93 - 145
2	3	1	MET	MET	LEU	LEU	B	B	73 - 125	93 - 145
3	3	1	MET	MET	LEU	LEU	C	C	73 - 125	93 - 145
4	3	1	MET	MET	LEU	LEU	D	D	73 - 125	93 - 145
1	4	1	ASP	ASP	LEU	LEU	A	A	134 - 201	154 - 221
2	4	1	ASP	ASP	LEU	LEU	B	B	134 - 201	154 - 221
3	4	1	ASP	ASP	LEU	LEU	C	C	134 - 201	154 - 221
4	4	1	ASP	ASP	LEU	LEU	D	D	134 - 201	154 - 221
1	5	1	TYR	TYR	PHE	PHE	A	A	228 - 276	248 - 296
2	5	1	TYR	TYR	PHE	PHE	B	B	228 - 276	248 - 296
3	5	1	TYR	TYR	PHE	PHE	C	C	228 - 276	248 - 296
4	5	1	TYR	TYR	PHE	PHE	D	D	228 - 276	248 - 296
1	6	1	LYS	LYS	ASP	ASP	A	A	600 - 620	620 - 640
2	6	1	LYS	LYS	ASP	ASP	B	B	600 - 620	620 - 640
3	6	1	LYS	LYS	ASP	ASP	C	C	600 - 620	620 - 640
4	6	1	LYS	LYS	ASP	ASP	D	D	600 - 620	620 - 640
1	1	2	HIS	HIS	ASP	ASP	A	A	300 - 598	320 - 618
2	1	2	HIS	HIS	ASP	ASP	B	B	300 - 598	320 - 618
3	1	2	HIS	HIS	ASP	ASP	C	C	300 - 598	320 - 618
4	1	2	HIS	HIS	ASP	ASP	D	D	300 - 598	320 - 618

NCS ensembles :

ID
1
2

#1: Protein

Glycogen [starch] synthase isoform 2

Mass: 81818.617 Da / Num. of mol.: 4 / Mutation: E169Q, A535S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GSY2, YLR258W, L8479.8 / Production host:

Escherichia coli (E. coli) / References: UniProt: P27472, glycogen(starch) synthase

#2: Chemical

ChemComp-UDP / URIDINE-5'-DIPHOSPHATE

Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM

#3: Sugar

ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose

Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P

#4: Sugar

ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃NO₅

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.11 Å³/Da / Density % sol: 64.83 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 6.1, 22 % Peg 300

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.98→145.5 Å / Num. obs: 98100 / % possible obs: 95.2 % / Redundancy: 4.3 % / Net I/σ(I): 14.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NB0

3nb0

Resolution: 2.98→30 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.918 / SU B: 42.149 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24407	4474	5.4 %	RANDOM
R_work	0.1957	-	-	-
obs	0.19825	78100	99.6 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 87.609 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1 Å²	-0 Å²	-0 Å²
2-	-	1.97 Å²	-0 Å²
3-	-	-	-0.96 Å²

Refinement step

Cycle: 1 / Resolution: 2.98→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20209	0	176	1	20386

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	20870
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	19461
X-RAY DIFFRACTION	r_angle_refined_deg	1.401	1.954	28368
X-RAY DIFFRACTION	r_angle_other_deg	0.961	3	44566
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.296	5	2542
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.121	23.707	1017
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.122	15	3354
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.937	15	139
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	3138
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	23712
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5053
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.598	5.339	10186
X-RAY DIFFRACTION	r_mcbond_other	1.596	5.338	10185
X-RAY DIFFRACTION	r_mcangle_it	2.788	8.006	12722
X-RAY DIFFRACTION	r_mcangle_other	2.788	8.006	12723
X-RAY DIFFRACTION	r_scbond_it	1.459	5.412	10684
X-RAY DIFFRACTION	r_scbond_other	1.459	5.412	10684
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.589	8.117	15647
X-RAY DIFFRACTION	r_long_range_B_refined	5.28	61.665	22952
X-RAY DIFFRACTION	r_long_range_B_other	5.28	61.666	22953
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1392	MEDIUM POSITIONAL	0.21	0.5
1	2	B	1392	MEDIUM POSITIONAL	0.2	0.5
1	3	C	1392	MEDIUM POSITIONAL	0.26	0.5
1	4	D	1392	MEDIUM POSITIONAL	0.21	0.5
1	1	A	2059	LOOSE POSITIONAL	0.72	5
1	2	B	2059	LOOSE POSITIONAL	0.78	5
1	3	C	2059	LOOSE POSITIONAL	0.75	5
1	4	D	2059	LOOSE POSITIONAL	0.85	5
1	1	A	1392	MEDIUM THERMAL	8.09	2
1	2	B	1392	MEDIUM THERMAL	19.26	2
1	3	C	1392	MEDIUM THERMAL	8.66	2
1	4	D	1392	MEDIUM THERMAL	19.96	2
1	1	A	2059	LOOSE THERMAL	8.42	10
1	2	B	2059	LOOSE THERMAL	19.57	10
1	3	C	2059	LOOSE THERMAL	9.48	10
1	4	D	2059	LOOSE THERMAL	20.9	10
2	1	A	1757	MEDIUM POSITIONAL	0.17	0.5
2	2	B	1757	MEDIUM POSITIONAL	0.23	0.5
2	3	C	1757	MEDIUM POSITIONAL	0.24	0.5
2	4	D	1757	MEDIUM POSITIONAL	0.16	0.5
2	1	A	2912	LOOSE POSITIONAL	0.6	5
2	2	B	2912	LOOSE POSITIONAL	0.59	5
2	3	C	2912	LOOSE POSITIONAL	0.6	5
2	4	D	2912	LOOSE POSITIONAL	0.57	5
2	1	A	1757	MEDIUM THERMAL	10.79	2
2	2	B	1757	MEDIUM THERMAL	11.15	2
2	3	C	1757	MEDIUM THERMAL	7.64	2
2	4	D	1757	MEDIUM THERMAL	7.49	2
2	1	A	2912	LOOSE THERMAL	11.36	10
2	2	B	2912	LOOSE THERMAL	11.6	10
2	3	C	2912	LOOSE THERMAL	7.85	10
2	4	D	2912	LOOSE THERMAL	7.89	10

LS refinement shell

Resolution: 2.984→3.061 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.376	295	-
R_work	0.325	5659	-
obs	-	-	97.37 %

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	1.3502	-0.3021	-0.4017	1.8455	-1.29	1.2703	0.1449	0.4738	0.0911	-0.2783	0.0349	0.1198	0.2928	-0.4173	-0.1798	0.3911	-0.1137	-0.0955	0.9812	-0.0501	0.0641	-78.9056	-58.7237	40.8767
2	0.229	0.0934	-0.2966	0.1459	0.0332	0.7037	0.0727	0.0386	0.0941	0.0236	0.011	-0.0026	-0.1023	-0.1494	-0.0837	0.2891	0.2103	0.0993	0.7113	0.0771	0.1858	-60.0034	-38.5921	18.0634
3	1.2135	-0.2245	-0.5375	2.4774	0.0114	0.2846	-0.2098	0.0384	-0.3812	0.2385	-0.0086	0.4405	0.0484	0.0837	0.2184	0.2767	-0.0007	0.1394	0.4861	0.0007	0.4436	-23.8238	-102.881	-23.9789
4	0.3207	-0.3016	-0.1224	0.7323	0.1424	0.0778	0.0333	0.0501	-0.0642	-0.06	-0.008	0.077	-0.0865	-0.0034	-0.0253	0.3276	0.0349	0.0035	0.6572	0.0325	0.1932	-25.3435	-66.002	-24.0826
5	1.1352	0.1873	0.093	1.1103	-0.3862	0.4445	-0.0792	-0.3547	0.2399	0.1652	-0.0002	-0.086	-0.2907	-0.2324	0.0793	0.316	0.1363	-0.098	0.7271	-0.1514	0.1594	-67.7662	-29.1795	-40.2428
6	0.111	-0.1387	0.2674	0.3124	-0.2308	0.8623	0.0148	-0.0274	-0.0548	-0.0178	0.021	0.0474	0.0033	-0.1875	-0.0358	0.1459	0.0439	-0.0103	0.8558	0.1043	0.1615	-65.7533	-57.0597	-25.8037
7	1.0366	0.5243	-0.2914	2.4033	-0.4941	0.1454	0.0855	-0.2648	0.4299	-0.1815	-0.0389	-0.133	-0.033	0.1101	-0.0466	0.3472	-0.322	-0.0317	0.4944	-0.0548	0.326	-3.975	-20.6334	21.8924
8	0.3996	0.1375	0.0652	0.0891	0.0323	0.4063	-0.0092	-0.1466	0.028	-0.0497	0.053	0.0552	-0.0429	0.0854	-0.0438	0.3238	0.0383	0.0414	0.6986	-0.0041	0.1647	-23.3489	-52.8156	20.848

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 275
2	X-RAY DIFFRACTION	2	A	276 - 639
3	X-RAY DIFFRACTION	3	B	2 - 275
4	X-RAY DIFFRACTION	4	B	276 - 639
5	X-RAY DIFFRACTION	5	C	2 - 220
6	X-RAY DIFFRACTION	6	C	221 - 639
7	X-RAY DIFFRACTION	7	D	2 - 276
8	X-RAY DIFFRACTION	8	D	277 - 639

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