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BMRB: 25565

2N1L

Solution structure of the BCOR PUFD

Authors

Wong, S.J., Gearhart, M.D., Ha, D.J., Corcoran, C.M., Diaz, V., Taylor, A.B., Schirf, V., Ilangovan, U., Hinck, A.P., Demeler, B., Hart, P.J., Bardwell, V.J., Kim, C.A.

Assembly

BCOR PUFD

Entity

1. BCOR PUFD (polymer, Thiol state: not present), 115 monomers, 13102.62 Da Detail

SDVFEFEFSE TPLLPSYNIQ VSVAQGPRNW LLLSDVLKKL KMSSRIFRSN FPNVEIVTIA EAEFYRQVSA SLLFSSSKDL EAFNPESKEL LDLVEFTNEI QTLLGSSVEW LHPSD

Formula weight

13102.62 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 80.8 %, Completeness (bb): 91.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.8 % (1116 of 1382)	78.7 % (563 of 715)	81.9 % (447 of 546)	87.6 % (106 of 121)
Backbone	91.4 % (620 of 678)	91.2 % (206 of 226)	91.5 % (314 of 343)	91.7 % (100 of 109)
Sidechain	73.4 % (600 of 817)	73.0 % (357 of 489)	75.0 % (237 of 316)	50.0 % (6 of 12)
Aromatic	16.4 % (22 of 134)	25.4 % (17 of 67)	7.7 % (5 of 65)	0.0 % (0 of 2)
Methyl	96.4 % (133 of 138)	95.7 % (66 of 69)	97.1 % (67 of 69)

1. BCOR PUFD

SDVFEFEFSE TPLLPSYNIQ VSVAQGPRNW LLLSDVLKKL KMSSRIFRSN FPNVEIVTIA EAEFYRQVSA SLLFSSSKDL EAFNPESKEL LDLVEFTNEI QTLLGSSVEW LHPSD

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 1 models in PDB: 2N1L, Strand ID: A Detail

Release date

2016-04-03

Citation

Structural basis for the hierarchical assembly of the core of PRC1.1
Wong, S.J., Gearhart, M.D., Ha, D.J., Corcoran, C.M., Diaz, V., Taylor, A.B., Schirf, V., Ilangovan, U., Hinck, A.P., Demeler, B., Hart, J.P., Bardwell, V.J., Kim, C.A.
Not known

Related entities 1. BCOR PUFD, : 1 : 4 : 12 entities Detail

Interaction partners 1. BCOR PUFD, : 35 interactors Detail

More details for 35 interactors identified by 8 citations

Experiments performed 8 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 8

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		3 mM
2	TRIS	natural abundance		10 mM
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25565_2n1l.nef
Input source #2: Coordindates	2n1l.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--------70--------80--------90-------100---
SDVFEFEFSETPLLPSYNIQVSVAQGPRNWLLLSDVLKKLKMSSRIFRSNFPNVEIVTIAEAEFYRQVSASLLFSSSKDLEAFNPESKELLDLVEFTNEI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SDVFEFEFSETPLLPSYNIQVSVAQGPRNWLLLSDVLKKLKMSSRIFRSNFPNVEIVTIAEAEFYRQVSASLLFSSSKDLEAFNPESKELLDLVEFTNEI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----110--------
QTLLGSSVEWLHPSD
|||||||||||||||
QTLLGSSVEWLHPSD
-------110-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_25565_2n1l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1109		95.7 (chain: A, length: 115)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	4281 (1)	noe	93.9 (chain: A, length: 115)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	Warning	208 (207)	.	96.5 (chain: A, length: 115)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	91 (91)	.	79.1 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 558
  - ¹³C chemical shifts: 446
  - ¹⁵N chemical shifts: 102
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 93.9%
- Total number of restraints: 4281
- Weight of restraints: 1.0 (4281)
- Potential type of restraints: square-well-parabolic (4281)
- Range of distance target values: 1.72, 4.13 (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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 96.5%
- Total number of restraints: 207
- Total number of restraints per polymer type: 207
- Weight of restraints: 1.0 (207)
- Potential type of restraints: square-well-parabolic (207)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 79.1%

-----10--------20--------30--------40--------50--------60--------70--------80--------90-------100---
SDVFEFEFSETPLLPSYNIQVSVAQGPRNWLLLSDVLKKLKMSSRIFRSNFPNVEIVTIAEAEFYRQVSASLLFSSSKDLEAFNPESKELLDLVEFTNEI
 |||||||  | || |||||||  || ||||||||||||||||  |||||| ||||||||||||||||||||||    |||||| || |||||||||  |
.DVFEFEF..T.LL.SYNIQVS..QG.RNWLLLSDVLKKLKMS..IFRSNF.NVEIVTIAEAEFYRQVSASLLF....DLEAFN.ES.ELLDLVEFT..I

----110--------
QTLLGSSVEWLHPSD
|||||   ||||  |
QTLLG...EWLH..D

Total number of restraints: 91
Potential type of restraints: undefined (91)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords PRC1, PcG, Polycomb