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Found 1 Document (1.074 seconds)

BMRB: 18952

2M3B

Serine 16 phosphorylated phospholamban pentamer, Hybrid solution and solid-state NMR structural ensemble

Authors

Vostrikov, V.V., Verardi, R., Veglia, G.

Assembly

Phospholamban

Entity

1. Phospholamban, entity (polymer), 52 monomers, 6174.436 × 5 Da Detail

MEKVQYLTRS AIRRAXTIEM PQQARQNLQN LFINFCLILI CLLLICIIVM LL

2. PHOSPHOSERINE (non-polymer, Thiol state: not present), 185.072 Da

Total weight

31057.252 Da

Max. entity weight

6174.436 Da

Source organism

Oryctolagus cuniculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.2 %, Completeness: 25.4 %, Completeness (bb): 65.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	25.4 % (101 of 397)	15.3 % (52 of 339)	84.5 % (49 of 58)
Backbone	65.6 % (99 of 151)	49.5 % (50 of 101)	98.0 % (49 of 50)
Sidechain	0.8 % (2 of 246)	0.8 % (2 of 238)	0.0 % (0 of 8)
Aromatic	0.0 % (0 of 14)	0.0 % (0 of 14)
Methyl	4.4 % (2 of 45)	4.4 % (2 of 45)

1. entity

MEKVQYLTRS AIRRAXTIEM PQQARQNLQN LFINFCLILI CLLLICIIVM LL

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Temperature 273 K, pH 6

#	Name	Isotope labeling	Concentration
1	Phospholamban	[U-100% 13C; U-100% 15N]	0.1 mM
2	DPC	[U-2H]	300 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	120 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Temperature 273 K, pH 6

#	Name	Isotope labeling	Concentration
9	Phospholamban	[U-13C; U-15N; U-2H]	0.15 mM
10	DPC	natural abundance	300 mM
11	sodium phosphate	natural abundance	20 mM
12	sodium chloride	natural abundance	120 mM
13	beta-mercaptoethanol	natural abundance	10 mM
14	sodium azide	natural abundance	0.02 %
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

Sample #3

Solvent system 100% H2O, Temperature 273 K, pH 6, Details Multiple samples with selective 15N labeling

#	Name	Isotope labeling	Concentration
17	Phospholamban	[U-100% 15N]	4 mg
18	DOPC	natural abundance	38 mg
19	DOPE	natural abundance	9 mg
20	D2O	natural abundance	100 %

Sample #4

Solvent system 100% H2O, Temperature 273 K, pH 6, Details Physical mixture of 13C/15N-Leu and 13C/15N-Ile samples

#	Name	Isotope labeling	Concentration
21	Phospholamban	[U-100% 13C; U-100% 15N]	1 mg
22	DOPC	natural abundance	12 mg
23	DOPE	natural abundance	3 mg
24	MOPS	natural abundance	20 mM
25	sodium chloride	natural abundance	50 mM
26	sodium azide	natural abundance	0.02 %
27	D2O	natural abundance	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M3B, Strand ID: A, B, C, D, E Detail

Release date

2013-10-23

Citation

Structural dynamics and topology of phosphorylated phospholamban homopentamer reveal its role in the regulation of calcium transport
Vostrikov, V.V., Mote, K.R., Verardi, R., Veglia, G.
Structure (2013), 21, 2119-2130, PubMed 24207128 , DOI 10.1016/j.str.2013.09.008 , Abstract

Related entities 1. Phospholamban, entity, : 1 : 11 : 7 entities Detail

Interaction partners 1. Phospholamban, entity, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 5 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, pH 6

#	Name	Isotope labeling	Concentration
1	Phospholamban	[U-100% 13C; U-100% 15N]	0.1 mM
2	DPC	[U-2H]	300 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	120 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

2 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, pH 6

#	Name	Isotope labeling	Concentration
1	Phospholamban	[U-100% 13C; U-100% 15N]	0.1 mM
2	DPC	[U-2H]	300 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	120 mM
5	beta-mercaptoethanol	natural abundance	10 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O	natural abundance	5 %

3 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Temperature 273 K, pH 6

#	Name	Isotope labeling	Concentration
9	Phospholamban	[U-13C; U-15N; U-2H]	0.15 mM
10	DPC	natural abundance	300 mM
11	sodium phosphate	natural abundance	20 mM
12	sodium chloride	natural abundance	120 mM
13	beta-mercaptoethanol	natural abundance	10 mM
14	sodium azide	natural abundance	0.02 %
15	H2O	natural abundance	95 %
16	D2O	natural abundance	5 %

4 2D PISEMA

Instrument

Bruker DMX - 600 MHz

Sample

State anisotropic, Solvent system 100% H2O, Temperature 273 K, pH 7, Details Multiple samples with selective 15N labeling

#	Name	Isotope labeling	Concentration
17	Phospholamban	[U-100% 15N]	4 mg
18	DOPC	natural abundance	38 mg
19	DOPE	natural abundance	9 mg
20	D2O	natural abundance	100 %

5 2D DARR

Instrument

Varian INOVA - 700 MHz

Sample

State solid, Solvent system 100% H2O, Temperature 273 K, pH 7, Details Physical mixture of 13C/15N-Leu and 13C/15N-Ile samples

#	Name	Isotope labeling	Concentration
21	Phospholamban	[U-100% 13C; U-100% 15N]	1 mg
22	DOPC	natural abundance	12 mg
23	DOPE	natural abundance	3 mg
24	MOPS	natural abundance	20 mM
25	sodium chloride	natural abundance	50 mM
26	sodium azide	natural abundance	0.02 %
27	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18952_2m3b.nef
Input source #2: Coordindates	2m3b.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:36:CYS:SG	E:41:CYS:SG	unknown	unknown	2.648
A:41:CYS:SG	B:36:CYS:SG	unknown	unknown	2.697
B:41:CYS:SG	C:36:CYS:SG	unknown	unknown	2.661
C:41:CYS:SG	D:36:CYS:SG	unknown	unknown	2.65
D:41:CYS:SG	E:36:CYS:SG	unknown	unknown	2.652

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)
1:15:ALA:C	1:16:SEP:N	unknown	unknown	n/a
1:16:SEP:C	1:17:THR:N	unknown	unknown	n/a
2:15:ALA:C	2:16:SEP:N	unknown	unknown	n/a
2:16:SEP:C	2:17:THR:N	unknown	unknown	n/a
3:15:ALA:C	3:16:SEP:N	unknown	unknown	n/a
3:16:SEP:C	3:17:THR:N	unknown	unknown	n/a
4:15:ALA:C	4:16:SEP:N	unknown	unknown	n/a
4:16:SEP:C	4:17:THR:N	unknown	unknown	n/a
5:15:ALA:C	5:16:SEP:N	unknown	unknown	n/a
5:16:SEP:C	5:17:THR:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	16	SEP	PHOSPHOSERINE	Coordinates
B	16	SEP	PHOSPHOSERINE	Assigned chemical shifts, Coordinates
C	16	SEP	PHOSPHOSERINE	Coordinates
D	16	SEP	PHOSPHOSERINE	Coordinates
E	16	SEP	PHOSPHOSERINE	Coordinates

Sequence alignments

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

--------10--------20--------30--------40--------50--
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL
||||||||||||||||||||||||||||||||||||||||||||||||||||
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL

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

--------10--------20--------30--------40--------50--
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL
||||||||||||||||||||||||||||||||||||||||||||||||||||
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL

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

--------10--------20--------30--------40--------50--
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL
||||||||||||||||||||||||||||||||||||||||||||||||||||
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL

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

--------10--------20--------30--------40--------50--
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL
||||||||||||||||||||||||||||||||||||||||||||||||||||
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL

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

--------10--------20--------30--------40--------50--
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL
||||||||||||||||||||||||||||||||||||||||||||||||||||
MEKVQYLTRSAIRRAXTIEMPQQARQNLQNLFINFCLILICLLLICIIVMLL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	52	100.0
B	B	52	100.0
C	C	52	100.0
D	D	52	100.0
E	E	52	100.0

Content subtype: combined_18952_2m3b.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	15		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	98		94.2 (chain: B, length: 52)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2510 (1)	noe	94.2 (chain: A, length: 52), 94.2 (chain: B, length: 52), 94.2 (chain: C, length: 52), 94.2 (chain: D, length: 52), 94.2 (chain: E, length: 52)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	158 (1)	undefined	9.6 (chain: A, length: 52), 9.6 (chain: B, length: 52), 9.6 (chain: C, length: 52), 9.6 (chain: D, length: 52), 9.6 (chain: E, length: 52)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	410 (410)	.	94.2 (chain: A, length: 52), 94.2 (chain: B, length: 52), 94.2 (chain: C, length: 52), 94.2 (chain: D, length: 52), 94.2 (chain: E, length: 52)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_8	Warning	70 (70)	.	26.9 (chain: A, length: 52), 26.9 (chain: B, length: 52), 26.9 (chain: C, length: 52), 26.9 (chain: D, length: 52), 26.9 (chain: E, length: 52)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 94.2%
- Total number of assignments
  - ¹H chemical shifts: 49
  - ¹⁵N chemical shifts: 49
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	343	49	14.3
¹⁵N chemical shifts	63	49	77.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	103	49	47.6
¹⁵N chemical shifts	51	49	96.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	240	0	0.0
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	14	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: D, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: E, Chain length: 52, Sequence coverage: 94.2%
- Total number of restraints: 2500
- Weight of restraints: 1.0 (2500)
- Potential type of restraints: square-well-parabolic (2500)
- Range of distance target values: 2.3, 3.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 9.6%
    - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 9.6%
    - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 9.6%
    - Entity_assembly_ID: D, Chain length: 52, Sequence coverage: 9.6%
    - Entity_assembly_ID: E, Chain length: 52, Sequence coverage: 9.6%
  - Total number of restraints: 158
  - Weight of restraints: 1.0 (158)
  - Potential type of restraints: square-well-parabolic (158)
  - Range of distance target values: 4.15, 4.15 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
    - Chain_ID: D
    - Chain_ID: E
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: D, Chain length: 52, Sequence coverage: 94.2%
  - Entity_assembly_ID: E, Chain length: 52, Sequence coverage: 94.2%
- Total number of restraints: 410
- Total number of restraints per polymer type: 410
- Weight of restraints: 1.0 (410)
- Potential type of restraints: square-well-parabolic (410)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_8
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 52, Sequence coverage: 26.9%
  - Entity_assembly_ID: B, Chain length: 52, Sequence coverage: 26.9%
  - Entity_assembly_ID: C, Chain length: 52, Sequence coverage: 26.9%
  - Entity_assembly_ID: D, Chain length: 52, Sequence coverage: 26.9%
  - Entity_assembly_ID: E, Chain length: 52, Sequence coverage: 26.9%
- Total number of restraints: 70
- Potential type of restraints: square-well-parabolic (70)
- Range of observed RDC values: -5.5, 8.3 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue

Keywords phospholamban, plb, pln

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Found 1 Document (1.074 seconds)

BMRB: 18952

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Phospholamban, entity, : 1 : 11 : 7 entities Detail

Interaction partners 1. Phospholamban, entity, : 1 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail