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Found 1 Document (0.603 seconds)

BMRB: 30493

6E4H

Solution NMR Structure of the Colied-coil PALB2 Homodimer

Authors

Song, F., Li, M., Liu, G., Swapna, G.V.T., Xia, B., Bunting, S.F., Montelione, G.T.

Assembly

Partner and localizer of BRCA2

Entity

1. Partner and localizer of BRCA2 (polymer, Thiol state: not present), 68 monomers, 7925.989 × 2 Da Detail

MEELSGKPLS YAEKEKLKEK LAFLKKEYSR TLARLQRAKR AEKAKNSKKA IEDGVPQPEA LEHHHHHH

Total weight

15851.978 Da

Max. entity weight

7925.989 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 86.8 %, Completeness: 77.4 %, Completeness (bb): 71.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.4 % (649 of 838)	83.5 % (375 of 449)	67.0 % (215 of 321)	86.8 % (59 of 68)
Backbone	71.9 % (289 of 402)	85.9 % (116 of 135)	57.9 % (117 of 202)	86.2 % (56 of 65)
Sidechain	82.7 % (415 of 502)	82.5 % (259 of 314)	82.7 % (153 of 185)	100.0 % (3 of 3)
Aromatic	52.0 % (26 of 50)	52.0 % (13 of 25)	52.0 % (13 of 25)
Methyl	89.7 % (52 of 58)	89.7 % (26 of 29)	89.7 % (26 of 29)

1. entity 1

MEELSGKPLS YAEKEKLKEK LAFLKKEYSR TLARLQRAKR AEKAKNSKKA IEDGVPQPEA LEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] PALB2cc, 20 mM MES, 200 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 10 % DSS, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 v/v [U-100% 13C; U-100% 15N] PALB2cc, 2 v/v unlabeled PALB2cc, 20 mM MES, 200 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 0.02 % sodium azide, 10 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	PALB2cc	[U-100% 13C; U-100% 15N]	1 v/v
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	200 mM
11	Calcium Chloride	natural abundance	5 mM
12	DTT	natural abundance	10 mM
13	DSS	natural abundance	10 %
14	sodium azide	natural abundance	0.02 %
15	unlabeled PALB2cc	natural abundance	2 v/v

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: -0.31 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: -0.31 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: -0.07 ppm, Outliers: 2 Detail

Release date

2018-08-14

Citation

Antiparallel Coiled-Coil Interactions Mediate Homodimerization of the DNA Damage Repair Protein, PALB2
Song, F., Li, M., Liu, G., Swapna, G.V.T., Daigham, N.S., Xia, B., Montelione, G.T., Bunting, S.F.
Biochemistry (2018), 57, 6581-6591, PubMed 30289697 , DOI 10.1021/acs.biochem.8b00789 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 30796 released on 2020-10-01
    Title Solution NMR Structure of the Coiled-coil BRCA1-PALB2 Heterodimer
  BMRB: 27534 released on 2018-07-05
    Title Solution NMR Structure of PALB2 Colied-coil Domain (PALB2cc)

Related entities 1. Partner and localizer of BRCA2, : 2 : 3 entities Detail

Experiments performed 15 experiments Detail

1 2D TROSY-HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] PALB2cc, 20 mM MES, 200 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 10 % DSS, 0.02 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

3 3D TROSY-HNCOCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

4 3D TROSY-HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

5 3D TROSY-HNCOCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

6 3D TROSY-HBHACONH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

7 3D TROSY-HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

9 AROMATIC CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

10 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

12 3D simultaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

14 X-filtered noesy (pulse sequence: noesyhsqcgpwgx13d)

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1 v/v [U-100% 13C; U-100% 15N] PALB2cc, 2 v/v unlabeled PALB2cc, 20 mM MES, 200 mM sodium chloride, 5 mM Calcium Chloride, 10 mM DTT, 0.02 % sodium azide, 10 % DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	PALB2cc	[U-100% 13C; U-100% 15N]	1 v/v
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	200 mM
11	Calcium Chloride	natural abundance	5 mM
12	DTT	natural abundance	10 mM
13	DSS	natural abundance	10 %
14	sodium azide	natural abundance	0.02 %
15	unlabeled PALB2cc	natural abundance	2 v/v

15 3D TROSY-HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PALB2cc	[U-100% 13C; U-100% 15N]	1.2 mM
2	MES	natural abundance	20 mM
3	sodium chloride	natural abundance	200 mM
4	Calcium Chloride	natural abundance	5 mM
5	DTT	natural abundance	10 mM
6	DSS	natural abundance	10 %
7	sodium azide	natural abundance	0.02 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30493_6e4h.nef
Input source #2: Coordindates	6e4h.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--------
MEELSGKPLSYAEKEKLKEKLAFLKKEYSRTLARLQRAKRAEKAKNSKKAIEDGVPQPEALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEELSGKPLSYAEKEKLKEKLAFLKKEYSRTLARLQRAKRAEKAKNSKKAIEDGVPQPEALEHHHHHH

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

--------10--------20--------30--------40--------50--------60--------
MEELSGKPLSYAEKEKLKEKLAFLKKEYSRTLARLQRAKRAEKAKNSKKAIEDGVPQPEALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEELSGKPLSYAEKEKLKEKLAFLKKEYSRTLARLQRAKRAEKAKNSKKAIEDGVPQPEALEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	68	0	0	100.0
B	B	68	0	0	100.0

Content subtype: combined_30493_6e4h.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	644		86.8 (chain: A, length: 68)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	4806 (1)	noe	89.7 (chain: A, length: 68), 89.7 (chain: B, length: 68)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	100 (1)	hbond	45.6 (chain: A, length: 68), 45.6 (chain: B, length: 68)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	164 (164)	.	79.4 (chain: A, length: 68), 79.4 (chain: B, length: 68)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 86.8%
- Total number of assignments
  - ¹H chemical shifts: 374
  - ¹³C chemical shifts: 211
  - ¹⁵N chemical shifts: 59
- 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	449	374	83.3
¹³C chemical shifts	321	211	65.7
¹⁵N chemical shifts	72	59	81.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	135	116	85.9
¹³C chemical shifts	136	58	42.6
¹⁵N chemical shifts	65	56	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	314	258	82.2
¹³C chemical shifts	185	153	82.7
¹⁵N chemical shifts	7	3	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	26	86.7
¹³C chemical shifts	30	26	86.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	13	52.0
¹³C chemical shifts	25	13	52.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 89.7%
  - Entity_assembly_ID: B, Chain length: 68, Sequence coverage: 89.7%
- Total number of restraints: 4789
- Weight of restraints: 1.0 (4789)
- Potential type of restraints: square-well-parabolic (4789)
- Range of distance target values: 2.23, 4.35 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 45.6%
    - Entity_assembly_ID: B, Chain length: 68, Sequence coverage: 45.6%
  - Total number of restraints: 100
  - Weight of restraints: 1.0 (100)
  - Potential type of restraints: square-well-parabolic (100)
  - Range of distance target values: 1.99, 2.99 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 79.4%
  - Entity_assembly_ID: B, Chain length: 68, Sequence coverage: 79.4%
- Total number of restraints: 164
- Total number of restraints per polymer type: 164
- Weight of restraints: 1.0 (164)
- Potential type of restraints: square-well-parabolic (164)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords Antiparallel Coiled coil, DNA Damage Repair, Homologous recombination, ONCOPROTEIN

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Found 1 Document (0.603 seconds)

BMRB: 30493

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. Partner and localizer of BRCA2, : 2 : 3 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail