BMRBj - BMREntryMaster

Found 1 Document (0.691 seconds)

BMRB: 30062

5J7J

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

Authors

Turner, M.L., Ames, J.B., Anderson, D.E.

Assembly

Calmodulin, Disks large homolog 4

Entity

1. Calmodulin (polymer, Thiol state: not present), 148 monomers, 16706.21 Da Detail

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

2. CALCIUM ION (non-polymer), 40.078 Da
3. PHOSPHOTHREONINE (non-polymer), 199.099 × 4 Da

Total weight

17542.686 Da

Max. entity weight

16706.21 Da

Source organism

Xenopus laevis

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 70.2 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	70.2 % (1172 of 1670)	65.4 % (567 of 867)	71.6 % (462 of 645)	90.5 % (143 of 158)
Backbone	96.0 % (849 of 884)	95.4 % (291 of 305)	96.1 % (416 of 433)	97.3 % (142 of 146)
Sidechain	49.2 % (454 of 923)	48.4 % (272 of 562)	51.9 % (181 of 349)	8.3 % (1 of 12)
Aromatic	10.0 % (10 of 100)	10.0 % (5 of 50)	10.0 % (5 of 50)
Methyl	41.5 % (59 of 142)	42.3 % (30 of 71)	40.8 % (29 of 71)

1. Calmodulin

ADQLTEEQIA EFKEAFSLFD KDGDGTITTK ELGTVMRSLG QNPTEAELQD MINEVDADGN GTIDFPEFLT MMARKMKDTD SEEEIREAFR VFDKDGNGYI SAAELRHVMT NLGEKLTDEE VDEMIREADI DGDGQVNYEE FVQMMTAK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7, Details 500 uM [U-100% 13C; U-100% 15N] Calmodulin, 750 uM PSD-95 phosphorylated, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

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: 0.15 ppm, Outliers: 2 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: 0.15 ppm, Outliers: 2 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: 0.17 ppm, Outliers: 3 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: -0.64 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 4 models in PDB: 5J7J, Strand ID: A Detail

Release date

2016-04-20

Citation

Ca²⁺/calmodulin binding to PSD-95 mediates homeostatic synaptic scaling down
Chowdhury, D., Turner, M., Patriarchi, T., Hergarden, A.C., Anderson, D., Zhang, Y., Sun, J., Chen, C.Y., Ames, J.B., Hell, J.W.
EMBO J. (2018), 37, 122-138, PubMed 29118000 , DOI 10.15252/embj.201695829 , Abstract

Related entities 1. Calmodulin, : 1 : 111 : 6 : 3 : 178 entities Detail

Interaction partners 1. Calmodulin, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7, Details 500 uM [U-100% 13C; U-100% 15N] Calmodulin, 750 uM PSD-95 phosphorylated, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

2 IPAP HSQC

Instrument

Bruker AvanceIII - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7, Details 500 uM [U-100% 13C; U-100% 15N] Calmodulin, 750 uM PSD-95 phosphorylated, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

3 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

4 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

5 3D CBCA(CO)NH

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

6 3D HNCO

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

7 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Calmodulin	[U-100% 13C; U-100% 15N]	500 uM
2	PSD-95 phosphorylated	natural abundance	750 uM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30062_5j7j.nef
Input source #2: Coordindates	5j7j.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:20:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:22:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:22:ASP:OD2	3:1:CA:CA	unknown	unknown	n/a
1:24:ASP:OD1	3:1:CA:CA	unknown	unknown	n/a
1:26:THR:O	3:1:CA:CA	unknown	unknown	n/a
1:31:GLU:OE1	3:1:CA:CA	unknown	unknown	n/a
1:31:GLU:OE2	3:1:CA:CA	unknown	unknown	n/a
1:56:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:58:ASP:OD1	3:2:CA:CA	unknown	unknown	n/a
1:58:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
1:60:ASN:OD1	3:2:CA:CA	unknown	unknown	n/a
1:62:THR:O	3:2:CA:CA	unknown	unknown	n/a
1:64:ASP:OD2	3:2:CA:CA	unknown	unknown	n/a
1:67:GLU:OE1	3:2:CA:CA	unknown	unknown	n/a
1:67:GLU:OE2	3:2:CA:CA	unknown	unknown	n/a
1:93:ASP:OD1	3:3:CA:CA	unknown	unknown	n/a
1:95:ASP:OD1	3:3:CA:CA	unknown	unknown	n/a
1:95:ASP:OD2	3:3:CA:CA	unknown	unknown	n/a
1:97:ASN:OD1	3:3:CA:CA	unknown	unknown	n/a
1:99:TYR:O	3:3:CA:CA	unknown	unknown	n/a
1:104:GLU:OE1	3:3:CA:CA	unknown	unknown	n/a
1:104:GLU:OE2	3:3:CA:CA	unknown	unknown	n/a
1:129:ASP:OD1	3:4:CA:CA	unknown	unknown	n/a
1:131:ASP:OD1	3:4:CA:CA	unknown	unknown	n/a
1:133:ASP:OD2	3:4:CA:CA	unknown	unknown	n/a
1:135:GLN:O	3:4:CA:CA	unknown	unknown	n/a
1:140:GLU:OE1	3:4:CA:CA	unknown	unknown	n/a
1:140:GLU:OE2	3:4:CA:CA	unknown	unknown	n/a
2:18:ASP:C	2:19:TPO:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	19	TPO	PHOSPHOTHREONINE	Coordinates
C	1	CA	CALCIUM ION	None
C	2	CA	CALCIUM ION	None
C	3	CA	CALCIUM ION	None
C	4	CA	CALCIUM ION	None

Sequence alignments

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

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

-------110-------120-------130-------140--------
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
||||||||||||||||||||||||||||||||||||||||||||||||
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

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

--------10---------
MDCLCIVTTKKYRYQDEDX
|||||||||||||||||||
MDCLCIVTTKKYRYQDEDX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0
B	B	19	0	0	100.0

Content subtype: combined_30062_5j7j.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	29		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1106		99.3 (chain: A, length: 148)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	35 (1)	noe	5.4 (chain: A, length: 148), 68.4 (chain: B, length: 19)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 99.3%
- Total number of assignments
  - ¹H chemical shifts: 523
  - ¹³C chemical shifts: 440
  - ¹⁵N chemical shifts: 143
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	867	523	60.3
¹³C chemical shifts	645	440	68.2
¹⁵N chemical shifts	164	143	87.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	305	295	96.7
¹³C chemical shifts	296	285	96.3
¹⁵N chemical shifts	146	143	97.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	562	228	40.6
¹³C chemical shifts	349	155	44.4
¹⁵N chemical shifts	18	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	29	36.2
¹³C chemical shifts	80	29	36.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	0	0.0
¹³C chemical shifts	50	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 5.4%
  - Entity_assembly_ID: B, Chain length: 19, Sequence coverage: 68.4%
- Total number of restraints: 35
- Weight of restraints: 1.0 (35)
- Potential type of restraints: square-well-parabolic (35)
- Range of distance target values: 1.0, 1.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Keywords METAL BINDING PROTEIN, PSD-95, Voltage-Gated Channel, calmodulin, phosphorylated

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Found 1 Document (0.691 seconds)

BMRB: 30062

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Calmodulin, : 1 : 111 : 6 : 3 : 178 entities Detail

Interaction partners 1. Calmodulin, : 1 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 3 contents Detail