BMRBj - BMREntryMaster

Found 1 Document (1.123 seconds)

BMRB: 19399

2MBH

NMR structure of EKLF(22-40)/Ubiquitin Complex

Authors

Raiola, L., Omichinski, J.G.

Assembly

EKLF(22-40)/Ubiquitin Complex

Entity

1. EKLF (polymer, Thiol state: not present), 19 monomers, 2357.466 Da Detail

DTQDDFLKWW RSEEAQDMG

2. Ubiquitin (polymer, Thiol state: not present), 76 monomers, 8564.731 Da Detail

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Total weight

10922.197 Da

Max. entity weight

8564.731 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.7 %, Completeness (bb): 84.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.7 % (1009 of 1138)	95.5 % (571 of 598)	77.5 % (338 of 436)	96.2 % (100 of 104)
Backbone	84.2 % (475 of 564)	96.4 % (187 of 194)	71.6 % (199 of 278)	96.7 % (89 of 92)
Sidechain	93.8 % (621 of 662)	95.0 % (384 of 404)	91.9 % (226 of 246)	91.7 % (11 of 12)
Aromatic	65.2 % (43 of 66)	81.8 % (27 of 33)	45.2 % (14 of 31)	100.0 % (2 of 2)
Methyl	97.2 % (103 of 106)	96.2 % (51 of 53)	98.1 % (52 of 53)

1. EKLF

DTQDDFLKWW RSEEAQDMG

2. Ubiquitin

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	Ubi_unl	natural abundance	4 mM
2	EKLF	[U-100% 15N]	0.8 mM
3	H2O	natural abundance	90 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
5	EKLF_unl	natural abundance	4 mM
6	Ubiquitin	[U-100% 15N]	0.8 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	EKLF_unl	natural abundance	4 mM
10	Ubiquitin	[U-100% 13C; U-100% 15N]	0.8 mM
11	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Temperature 300 K, pH 6.5

#	Name	Isotope labeling	Concentration
12	Ubi_unl	natural abundance	4 mM
13	phosphate buffer	natural abundance	20 mM
14	EKLF	[U-100% 13C; U-100% 15N]	0.8 mM
15	D2O	natural abundance	100 %

Protein Blocks Logo

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

Release date

2013-10-07

Citation

Structural characterization of a noncovalent complex between ubiquitin and the transactivation domain of the erythroid-specific factor EKLF
Raiola, L., Lussier-Price, M., Gagnon, D., Lafrance-Vanasse, J., Mascle, X., Arseneault, G., Legault, P., Archambault, J., Omichinski, J.G.
Structure (2013), 21, 2014-2024, PubMed 24139988 , DOI 10.1016/j.str.2013.08.027 , Abstract

Related entities 1. EKLF, : 1 : 3 : 6 entities Detail

Related entities 2. Ubiquitin, : 92 : 6 : 47 : 182 entities Detail

Interaction partners 1. EKLF, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19399_2mbh.nef
Input source #2: Coordindates	2mbh.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
Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
B	B	41	0	0	100.0
A	A	76	0	0	100.0

Content subtype: combined_19399_2mbh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1023		100.0 (chain: A, length: 76), 46.3 (chain: B, length: 41)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1659 (1)	noe	100.0 (chain: A, length: 76)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	54 (1)	hbond	47.4 (chain: A, length: 76)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	91 (91)	.	59.2 (chain: A, length: 76), 36.6 (chain: B, length: 41)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 41, Sequence coverage: 46.3%
- Total number of assignments
  - ¹H chemical shifts: 583
  - ¹³C chemical shifts: 339
  - ¹⁵N chemical shifts: 101
- 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
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	478	464	97.1
¹³C chemical shifts	350	256	73.1
¹⁵N chemical shifts	85	77	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	152	98.1
¹³C chemical shifts	152	74	48.7
¹⁵N chemical shifts	73	70	95.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	312	96.6
¹³C chemical shifts	198	182	91.9
¹⁵N chemical shifts	12	7	58.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0
¹³C chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	11	68.8
¹³C chemical shifts	16	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 100.0%
- Total number of restraints: 1647
- Weight of restraints: 1.0 (1647)
- Potential type of restraints: square-well-parabolic (1647)
- Range of distance target values: 1.4, 4.2 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 76, Sequence coverage: 47.4%
  - Total number of restraints: 54
  - Weight of restraints: 1.0 (54)
  - Potential type of restraints: square-well-parabolic (54)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - 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: 76, Sequence coverage: 59.2%
  - Entity_assembly_ID: B, Chain length: 41, Sequence coverage: 36.6%
- Total number of restraints: 91
- Total number of restraints per polymer type: 91
- Weight of restraints: 1.0 (91)
- Potential type of restraints: square-well-parabolic (91)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords EKLF, Protein-protein complex, transcription factor TAD, Ubiquitin, UIM/MIU

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.123 seconds)

BMRB: 19399

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. EKLF, : 1 : 3 : 6 entities Detail

Related entities 2. Ubiquitin, : 92 : 6 : 47 : 182 entities Detail

Interaction partners 1. EKLF, : 2 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail