BMRBj - BMREntryMaster

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BMRB: 25923

2NA1

ULD complex

Authors

Cierpicki, T., Gray, F., Cho, H.

Assembly

BMI1-PHC2 complex

Entity

1. BMI1-PHC2 complex (polymer), 155 monomers, 18199.02 Da Detail

GPAMGKPQIL THVIEGFVIQ EGAEPFPVGR SSLLVGNLKG DKRIITDDEI ISLSIEFFDQ NRLDRKVNKD KEKSKEEVND KRYLRCPAAM TVMHLRKFLR SKMDIPNTFQ IDVMYEEEPL KDYYTLMDIA YIYTWRRNGP LPLKYRVRPT CKRMK

Formula weight

18199.02 Da

Source organism

Exptl. method

Refine. method

conformational sampling

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.9 %, Completeness: 60.5 %, Completeness (bb): 88.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	60.5 % (1158 of 1915)	50.1 % (509 of 1015)	69.2 % (515 of 744)	85.9 % (134 of 156)
Backbone	88.0 % (801 of 910)	85.1 % (262 of 308)	88.8 % (406 of 457)	91.7 % (133 of 145)
Sidechain	41.7 % (480 of 1152)	34.9 % (247 of 707)	53.5 % (232 of 434)	9.1 % (1 of 11)
Aromatic	26.5 % (36 of 136)	29.4 % (20 of 68)	22.4 % (15 of 67)	100.0 % (1 of 1)
Methyl	83.7 % (134 of 160)	87.5 % (70 of 80)	80.0 % (64 of 80)

1. entity

GPAMGKPQIL THVIEGFVIQ EGAEPFPVGR SSLLVGNLKG DKRIITDDEI ISLSIEFFDQ NRLDRKVNKD KEKSKEEVND KRYLRCPAAM TVMHLRKFLR SKMDIPNTFQ IDVMYEEEPL KDYYTLMDIA YIYTWRRNGP LPLKYRVRPT CKRMK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

LACS Plot; CA

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 3.1 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2NA1, Strand ID: A Detail

Release date

2016-11-13

Citation

BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization
Gray, F., Cho, H., Shulka, S., He, S., Harris, A., Boytsov, B., Jaremko, L., Jaremko, M., Demeler, B., Lawlor, E.R., Grembecka, J., Cierpicki, T.
Nat. Commun. (2016), 7, 13343-13343, PubMed 27827373 , DOI 10.1038/ncomms13343 , Abstract

Related entities 1. BMI1-PHC2 complex, : 2 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

6 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303.2 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.2 mM
2	D2O	[U-2H]		10 %
3	sodium chloride	natural abundance		50 mM
4	TCEP	natural abundance		1 mM
5	TRIS	natural abundance		100 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25923_2na1.nef
Input source #2: Coordindates	2na1.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

----30--------40--------50--------60-----------130-------140-------150-------160-------170-------180
GPAMGKPQILTHVIEGFVIQEGAEPFPVGRSSLLVGNLKGDKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPAMGKPQILTHVIEGFVIQEGAEPFPVGRSSLLVGNLKGDKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------190-------200-------210-------220-------230-----
SKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
SKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMK
-------110-------120-------130-------140-------150-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	155	0	0	100.0

Content subtype: combined_25923_2na1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1011		90.3 (chain: A, length: 155)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	68 (1)	noe	14.8 (chain: A, length: 155)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	32 (1)	hbond	4.5 (chain: A, length: 155)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	Warning	26 (26)	.	11.6 (chain: A, length: 155)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 90.3%
- Total number of assignments
  - ¹³C chemical shifts: 469
  - ¹H chemical shifts: 413
  - ¹⁵N chemical shifts: 129
- 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: DYANA/DIANA_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 14.8%
- Total number of restraints: 68
- Weight of restraints: 1.0 (68)
- Potential type of restraints: upper-bound-parabolic (68)
- Range of distance target values: 1.8, 5.5 (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
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 4.5%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: upper-bound-parabolic (32)
  - Range of distance target values: 1.8, 3.0 (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: DYANA/DIANA_dihedral_2
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 11.6%
- Total number of restraints: 26
- Total number of restraints per polymer type: 26
- Weight of restraints: 1.0 (26)
- Potential type of restraints: square-well-parabolic (26)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords bmi1, phc2