BMRB Entry 18508

Name: Solution NMR structure of the beta2 carbohydrate module of AMP-activated protein kinase bound to glucosyl-cyclodextrin
Published: 2012-08-23

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PDB ID: 2lu4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18508
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2012-06-08

Original release date:

2012-08-23

Authors:

Gooley, Paul; Koay, Ann; Stapleton, David

Citation:

Citation: Bieri, Michael; Mobbs, Jesse; Koay, Ann; Louey, Gavin; Mok, Yee-Foong; Hatters, Danny; Park, Jong-Tae; Park, Kwan-Hwa; Neumann, Dietbert; Stapleton, David; Gooley, Paul. "AMP-activated protein kinase beta-subunit requires internal motion for optimal carbohydrate binding." Biophys. J. 102, 305-314 (2012).
PubMed: 22339867

Assembly members:

Assembly members:
entity, polymer, 105 residues, 11826.329 Da.

Natural source:

Natural source: Common Name: Rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pProEXHTc

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GAMGIRNSDSVKPTQQARPT VIRWSEGGKEVFISGSFNNW STKIPLIKSHNDFVAILDLP EGEHQYKFFVDGQWVHDPSE PVVTSQLGTINNLIHVKKSD FEVFD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	395
15N chemical shifts	106
1H chemical shifts	698

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	beta2 carbohydrate module of AMP-activated protein kinase	1

Entities:

Entity 1, beta2 carbohydrate module of AMP-activated protein kinase 105 residues - 11826.329 Da.

1

GLY

ALA

MET

GLY

ILE

ARG

ASN

SER

ASP

SER

2

VAL

LYS

PRO

THR

GLN

ALA

ARG

PRO

THR

3

VAL

ILE

ARG

TRP

SER

GLU

GLY

LYS

GLU

4

VAL

PHE

ILE

SER

GLY

SER

PHE

ASN

TRP

5

SER

THR

LYS

ILE

PRO

LEU

ILE

LYS

SER

HIS

6

ASN

ASP

PHE

VAL

ALA

ILE

LEU

ASP

LEU

PRO

7

GLU

GLY

GLU

HIS

GLN

TYR

LYS

PHE

VAL

8

ASP

GLY

GLN

TRP

VAL

HIS

ASP

PRO

SER

GLU

9

PRO

VAL

THR

SER

GLN

LEU

GLY

THR

ILE

10

ASN

LEU

ILE

HIS

VAL

LYS

SER

ASP

11

PHE

GLU

VAL

PHE

ASP

Samples:

sample_1: entity, [U-98% 15N], 0.7 ± 0.1 mM; sodium phosphate 50 mM; glucosyl-cyclodextrin 2.5 ± 0.1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_2: entity, [U-98% 13C; U-98% 15N], 0.7 ± 0.1 mM; sodium phosphate 50 mM; glucosyl-cyclodextrin 2.5 ± 0.1 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_3: entity 0.7 ± 0.1 mM; sodium phosphate 50 mM; glucosyl-cyclodextrin 2.5 ± 0.1 mM; sodium azide 0.02%; D2O 100%

sample_4: entity, [U-98% 13C; U-98% 15N], 0.7 ± 0.1 mM; sodium phosphate 50 mM; glucosyl-cyclodextrin 2.5 ± 0.1 mM; sodium azide 0.02%; D2O 100%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.9; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_4	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D HACAHB-COSY	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D13C,15N-filtered,edited NOESY	sample_4	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

SPARKY, Goddard - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz

BMRB	18507
PDB	2F15 2LU3 2LU4 4RER 4REW 4Y0G 4YEE
DBJ	BAE90075 BAF85509
EMBL	CAA12030 CAH72644 CAH90491
GB	AAF01293 AAH53610 AAH60228 AAH78821 AAM74153
REF	NP_001075383 NP_001125257 NP_001179257 NP_001230612 NP_005390
SP	O43741 Q6PAM0 Q9QZH4
TPG	DAA31622
AlphaFold	O43741 Q6PAM0 Q9QZH4