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BMRB: 19988

2MPL

Solution structure of the PR domain of FOG-1

Authors

Mackay, J.P., Clifton, M.K., Westman, B.J., Blobel, G.A.

Assembly

PR domain of FOG-1

Entity

1. PR domain of FOG-1 (polymer), 127 monomers, 14046.82 Da Detail

PWSGPEELEL ALQDGQRCVR ARLSLTEGLS WGPFYGSIQT RALSPEREEP GPAVTLMVDE SCWLRMLPQV LTEEAANSEI YRKDDALWCR VTKVVPSGGL LYVRLVTEPH GAPRHPVQEP VEPGGLA

Formula weight

14046.82 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.1 %, Completeness: 84.3 %, Completeness (bb): 91.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.3 % (1220 of 1447)	82.5 % (623 of 755)	85.4 % (485 of 568)	90.3 % (112 of 124)
Backbone	91.4 % (673 of 736)	91.3 % (230 of 252)	91.1 % (337 of 370)	93.0 % (106 of 114)
Sidechain	79.1 % (654 of 827)	78.1 % (393 of 503)	81.2 % (255 of 314)	60.0 % (6 of 10)
Aromatic	81.1 % (73 of 90)	91.1 % (41 of 45)	68.3 % (28 of 41)	100.0 % (4 of 4)
Methyl	86.3 % (126 of 146)	94.5 % (69 of 73)	78.1 % (57 of 73)

1. FOG-1 PR

PWSGPEELEL ALQDGQRCVR ARLSLTEGLS WGPFYGSIQT RALSPEREEP GPAVTLMVDE SCWLRMLPQV LTEEAANSEI YRKDDALWCR VTKVVPSGGL LYVRLVTEPH GAPRHPVQEP VEPGGLA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	FOG-1 PR	natural abundance		0.5-1 mM
2	sodium phosphate	natural abundance		20 mM
3	DSS	natural abundance		0.01 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	FOG-1 PR	[U-100% 15N]		0.5-1 mM
5	sodium phosphate	natural abundance		20 mM
6	DSS	natural abundance		0.01 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

LACS Plot; CA

Referencing offset: 0.01 ppm, Outliers: 4 Detail

LACS Plot; CB

Referencing offset: 0.01 ppm, Outliers: 4 Detail

LACS Plot; HA

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.46 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MPL, Strand ID: A Detail

Release date

2014-09-28

Citation

The identification and structure of an N-terminal PR domain show that FOG1 is a member of the PRDM family of proteins
Clifton, M.K., Westman, B.J., Thong, S., O'Connell, M.R., Shepherd, N.E., Quinlan, K.G., Crossley, M., Blobel, G.A., Mackay, J.P.
PLoS One (2014), 9, e106011-e106011, PubMed 25162672 , DOI 10.1371/journal.pone.0106011 , Abstract

Related entities 1. PR domain of FOG-1, : 1 : 2 : 7 entities Detail

Interaction partners 1. PR domain of FOG-1, : 5 interactors Detail

More details for 5 interactors identified by 2 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
4	FOG-1 PR	[U-100% 15N]		0.5-1 mM
5	sodium phosphate	natural abundance		20 mM
6	DSS	natural abundance		0.01 mM

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	FOG-1 PR	natural abundance		0.5-1 mM
2	sodium phosphate	natural abundance		20 mM
3	DSS	natural abundance		0.01 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

5 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

7 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

8 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

10 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

12 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

13 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

14 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5-1 mM in 20 mM Na2HPO4/NaH2PO4, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	FOG-1 PR	[U-100% 13C; U-100% 15N]		0.5-1 mM
8	sodium phosphate	natural abundance		20 mM
9	DSS	natural abundance		0.01 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19988_2mpl.nef
Input source #2: Coordindates	2mpl.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

100-----110-------120-------130-------140-------150-------160-------170-------180-------190-------20
PWSGPEELELALQDGQRCVRARLSLTEGLSWGPFYGSIQTRALSPEREEPGPAVTLMVDESCWLRMLPQVLTEEAANSEIYRKDDALWCRVTKVVPSGGL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PWSGPEELELALQDGQRCVRARLSLTEGLSWGPFYGSIQTRALSPEREEPGPAVTLMVDESCWLRMLPQVLTEEAANSEIYRKDDALWCRVTKVVPSGGL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------210-------220------
LYVRLVTEPHGAPRHPVQEPVEPGGLA
|||||||||||||||||||||||||||
LYVRLVTEPHGAPRHPVQEPVEPGGLA
-------110-------120-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_19988_2mpl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1189		89.8 (chain: A, length: 127)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1723 (1)	noe	86.6 (chain: A, length: 127)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	178 (178)	.	83.5 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 89.8%
- Total number of assignments
  - ¹H chemical shifts: 606
  - ¹³C chemical shifts: 474
  - ¹⁵N chemical shifts: 109
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 86.6%
- Total number of restraints: 1723
- Weight of restraints: 1.0 (1723)
- Potential type of restraints: square-well-parabolic (1723)
- Range of distance target values: 1.2, 2.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- 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: 127, Sequence coverage: 83.5%
- Total number of restraints: 178
- Total number of restraints per polymer type: 178
- Weight of restraints: 1.0 (178)
- Potential type of restraints: square-well-parabolic (178)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords FOG-1, GATA-1, PR domain, transcription, zinc-finger protein