BMRB Entry 30062

Name: NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated PSD-95
Published: 2017-10-19

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PDB ID: 5j7j
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30062
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated PSD-95

Deposition date:

2016-04-06

Original release date:

2017-10-19

Authors:

Turner, M.; Ames, J.; Anderson, D.

Citation:

Citation: Chowdhury, Dhrubajyoti; Turner, Matthew; Patriarchi, Tommaso; Hergarden, Anne; Anderson, David; Zhang, Yonghong; Sun, Junqing; Chen, Chao-Yin; Ames, James; Hell, Johannes. "Ca2+/calmodulin binding to PSD-95 mediates homeostatic synaptic scaling down" EMBO J. 37, 122-138 (2018).
PubMed: 29118000

Assembly members:

Assembly members:
Calmodulin, polymer, 148 residues, 16721.350 Da.
CALCIUM ION, non-polymer, 40.078 Da.
PHOSPHOTHREONINE, non-polymer, 199.099 Da.

Natural source:

Natural source: Common Name: African clawed frog Taxonomy ID: 8355 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Xenopus laevis

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Calmodulin: ADQLTEEQIAEFKEAFSLFD KDGDGTITTKELGTVMRSLG QNPTEAELQDMINEVDADGN GTIDFPEFLTMMARKMKDTD SEEEIREAFRVFDKDGNGYI SAAELRHVMTNLGEKLTDEE VDEMIREADIDGDGQVNYEE FVQMMTAK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	440
15N chemical shifts	143
1H chemical shifts	580

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	CALCIUM ION	2
3	PHOSPHOTHREONINE, 1	3
4	PHOSPHOTHREONINE, 2	3
5	PHOSPHOTHREONINE, 3	3
6	PHOSPHOTHREONINE, 4	3

Entities:

Entity 1, entity_1 148 residues - 16721.350 Da.

1

ALA

ASP

GLN

LEU

THR

GLU

GLN

ILE

ALA

2

GLU

PHE

LYS

GLU

ALA

PHE

SER

LEU

PHE

ASP

3

LYS

ASP

GLY

ASP

GLY

THR

ILE

THR

LYS

4

GLU

LEU

GLY

THR

VAL

MET

ARG

SER

LEU

GLY

5

GLN

ASN

PRO

THR

GLU

ALA

GLU

LEU

GLN

ASP

6

MET

ILE

ASN

GLU

VAL

ASP

ALA

ASP

GLY

ASN

7

GLY

THR

ILE

ASP

PHE

PRO

GLU

PHE

LEU

THR

8

MET

ALA

ARG

LYS

MET

LYS

ASP

THR

ASP

9

SER

GLU

ILE

ARG

GLU

ALA

PHE

ARG

10

VAL

PHE

ASP

LYS

ASP

GLY

ASN

GLY

TYR

ILE

11

SER

ALA

GLU

LEU

ARG

HIS

VAL

MET

THR

12

ASN

LEU

GLY

GLU

LYS

LEU

THR

ASP

GLU

13

VAL

ASP

GLU

MET

ILE

ARG

GLU

ALA

ASP

ILE

14

ASP

GLY

ASP

GLY

GLN

VAL

ASN

TYR

GLU

15

PHE

VAL

GLN

MET

THR

ALA

LYS

Entity 2, CALCIUM ION - 40.078 Da.

1

CA

Entity 3, PHOSPHOTHREONINE, 1 - 199.099 Da.

1

TPO

Samples:

sample_1: Calmodulin, [U-100% 13C; U-100% 15N], 500 uM; PSD-95 phosphorylated 750 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 318 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
IPAP HSQC	sample_1	anisotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1

Software:

HADDOCK, Bonvin - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AvanceIII 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks