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Found 1 Document (1.662 seconds)

BMRB: 18508

2LU4

Solution NMR structure of the beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin

Authors

Gooley, P., Koay, A., Stapleton, D.

Assembly

beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin

Entity

1. beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin (polymer, Thiol state: not present), 105 monomers, 11812.09 Da Detail

GAMGIRNSDS VKPTQQARPT VIRWSEGGKE VFISGSFNNW STKIPLIKSH NDFVAILDLP EGEHQYKFFV DGQWVHDPSE PVVTSQLGTI NNLIHVKKSD FEVFD

Formula weight

11812.09 Da

Source organism

Rattus norvegicus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.0 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.0 % (1094 of 1243)	91.9 % (593 of 645)	81.6 % (396 of 485)	92.9 % (105 of 113)
Backbone	94.8 % (586 of 618)	94.3 % (200 of 212)	95.4 % (293 of 307)	93.9 % (93 of 99)
Sidechain	83.8 % (605 of 722)	90.8 % (393 of 433)	72.7 % (200 of 275)	85.7 % (12 of 14)
Aromatic	43.8 % (57 of 130)	83.1 % (54 of 65)	0.0 % (0 of 62)	100.0 % (3 of 3)
Methyl	93.5 % (101 of 108)	94.4 % (51 of 54)	92.6 % (50 of 54)

1. entity

GAMGIRNSDS VKPTQQARPT VIRWSEGGKE VFISGSFNNW STKIPLIKSH NDFVAILDLP EGEHQYKFFV DGQWVHDPSE PVVTSQLGTI NNLIHVKKSD FEVFD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 15N]	0.7 (±0.1) mM
2	sodium phosphate	natural abundance	50 mM
3	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
4	sodium azide	natural abundance	0.02 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
8	sodium phosphate	natural abundance	50 mM
9	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
10	sodium azide	natural abundance	0.02 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity	natural abundance	0.7 (±0.1) mM
14	sodium phosphate	natural abundance	50 mM
15	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
16	sodium azide	natural abundance	0.02 %
17	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
18	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
19	sodium phosphate	natural abundance	50 mM
20	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
21	sodium azide	natural abundance	0.02 %
22	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 4 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.56 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LU4, Strand ID: A Detail

Release date

2012-08-22

Citation

AMP-activated protein kinase β-subunit requires internal motion for optimal carbohydrate binding
Bieri, M., Mobbs, J.I., Koay, A., Louey, G., Mok, Y., Hatters, D.M., Park, J., Park, K., Neumann, D., Stapleton, D., Gooley, P.R.
Biophys. J. (2012), 102, 305-314, PubMed 22339867 , DOI 10.1016/j.bpj.2011.12.012 , Abstract

Related entities 1. beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin, : 1 : 1 : 9 : 60 entities Detail

Interaction partners 1. beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin, : 67 interactors Detail

More details for 67 interactors identified by 11 citations

Experiments performed 16 experiments Detail

1 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
8	sodium phosphate	natural abundance	50 mM
9	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
10	sodium azide	natural abundance	0.02 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

2 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
8	sodium phosphate	natural abundance	50 mM
9	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
10	sodium azide	natural abundance	0.02 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
8	sodium phosphate	natural abundance	50 mM
9	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
10	sodium azide	natural abundance	0.02 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
8	sodium phosphate	natural abundance	50 mM
9	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
10	sodium azide	natural abundance	0.02 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

5 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
8	sodium phosphate	natural abundance	50 mM
9	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
10	sodium azide	natural abundance	0.02 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

6 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
7	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
8	sodium phosphate	natural abundance	50 mM
9	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
10	sodium azide	natural abundance	0.02 %
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
18	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
19	sodium phosphate	natural abundance	50 mM
20	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
21	sodium azide	natural abundance	0.02 %
22	D2O	natural abundance	100 %

8 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity	natural abundance	0.7 (±0.1) mM
14	sodium phosphate	natural abundance	50 mM
15	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
16	sodium azide	natural abundance	0.02 %
17	D2O	natural abundance	100 %

9 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
13	entity	natural abundance	0.7 (±0.1) mM
14	sodium phosphate	natural abundance	50 mM
15	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
16	sodium azide	natural abundance	0.02 %
17	D2O	natural abundance	100 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 15N]	0.7 (±0.1) mM
2	sodium phosphate	natural abundance	50 mM
3	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
4	sodium azide	natural abundance	0.02 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
18	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
19	sodium phosphate	natural abundance	50 mM
20	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
21	sodium azide	natural abundance	0.02 %
22	D2O	natural abundance	100 %

12 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 15N]	0.7 (±0.1) mM
2	sodium phosphate	natural abundance	50 mM
3	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
4	sodium azide	natural abundance	0.02 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

13 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 15N]	0.7 (±0.1) mM
2	sodium phosphate	natural abundance	50 mM
3	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
4	sodium azide	natural abundance	0.02 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

14 3D HACAHB-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
18	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
19	sodium phosphate	natural abundance	50 mM
20	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
21	sodium azide	natural abundance	0.02 %
22	D2O	natural abundance	100 %

15 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
1	entity	[U-98% 15N]	0.7 (±0.1) mM
2	sodium phosphate	natural abundance	50 mM
3	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
4	sodium azide	natural abundance	0.02 %
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

16 3D13C,15N-filtered,edited NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.9

#	Name	Isotope labeling	Concentration
18	entity	[U-98% 13C; U-98% 15N]	0.7 (±0.1) mM
19	sodium phosphate	natural abundance	50 mM
20	glucosyl-cyclodextrin	natural abundance	2.5 (±0.1) mM
21	sodium azide	natural abundance	0.02 %
22	D2O	natural abundance	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18508_2lu4.nef
Input source #2: Coordindates	2lu4.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GAMGIRNSDSVKPTQQARPTVIRWSEGGKEVFISGSFNNWSTKIPLIKSHNDFVAILDLPEGEHQYKFFVDGQWVHDPSEPVVTSQLGTINNLIHVKKSD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGIRNSDSVKPTQQARPTVIRWSEGGKEVFISGSFNNWSTKIPLIKSHNDFVAILDLPEGEHQYKFFVDGQWVHDPSEPVVTSQLGTINNLIHVKKSD

-----
FEVFD
|||||
FEVFD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0

Content subtype: combined_18508_2lu4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1097		100.0 (chain: A, length: 105)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2340 (1)	noe	94.3 (chain: A, length: 105)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	132 (132)	.	80.0 (chain: A, length: 105)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 395
  - ¹H chemical shifts: 596
  - ¹⁵N chemical shifts: 106
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
64	HIS	HE2	11.533
64	HIS	NE2	131.604

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	485	395	81.4
¹H chemical shifts	645	595	92.2
¹⁵N chemical shifts	116	105	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	210	195	92.9
¹H chemical shifts	212	202	95.3
¹⁵N chemical shifts	99	93	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	275	200	72.7
¹H chemical shifts	433	393	90.8
¹⁵N chemical shifts	17	12	70.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	55	50	90.9
¹H chemical shifts	55	51	92.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	62	0	0.0
¹H chemical shifts	65	54	83.1
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 94.3%
- Total number of restraints: 2340
- Weight of restraints: 1.0 (2340)
- Potential type of restraints: upper-bound-parabolic (2340)
- Range of distance target values: 2.3, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 80.0%
- Total number of restraints: 132
- Total number of restraints per polymer type: 132
- Weight of restraints: 1.0 (132)
- Potential type of restraints: square-well-parabolic (132)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords AMPK, carbohydrate binding module, CBM, glycogen binding

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Found 1 Document (1.662 seconds)

BMRB: 18508

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin, : 1 : 1 : 9 : 60 entities Detail

Interaction partners 1. beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin, : 67 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail