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BMRB: 34101

5N6R

Solution structure of the Dbl-homology domain of Bcr-Abl

Authors

Reckel, S., Lohr, F., Buchner, L., Guntert, P., Dotsch, V., Hantschel, O.

Assembly

Breakpoint cluster region protein (E.C.2.7.11.1)

Entity

1. Breakpoint cluster region protein (E.C.2.7.11.1) (polymer, Thiol state: all free), 218 monomers, 24812.12 Da Detail

AMASELDLEK GLEMRKWVLS GILASEETYL SHLEALLLPM KPLKAAATTS QPVLTSQQIE TIFFKVPELY EIHKEFYDGL FPRVQQWSHQ QRVGDLFQKL ASQLGVYRAF VDNYGVAMEM AEKCCQANAQ FAEISENLRA RSNKDAKDPT TKNSLETLLY KPVDRVTRST LVLHDLLKHT PASHPDHPLL QDALRISQNF LSSINEEITP RRQSMTVK

Formula weight

24812.12 Da

Source organism

Exptl. method

Refine. method

TORSION ANGLE DYNAMICS ONFORMERS, NUMBER CALCULATED : NULL

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.9 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.9 % (2544 of 2598)	97.6 % (1322 of 1355)	99.6 % (1009 of 1013)	92.6 % (213 of 230)
Backbone	99.0 % (1273 of 1286)	97.2 % (419 of 431)	99.8 % (647 of 648)	100.0 % (207 of 207)
Sidechain	97.3 % (1483 of 1524)	97.7 % (903 of 924)	99.5 % (574 of 577)	26.1 % (6 of 23)
Aromatic	99.4 % (179 of 180)	98.9 % (89 of 90)	100.0 % (88 of 88)	100.0 % (2 of 2)
Methyl	99.6 % (257 of 258)	99.2 % (128 of 129)	100.0 % (129 of 129)

1. entity 1

AMASELDLEK GLEMRKWVLS GILASEETYL SHLEALLLPM KPLKAAATTS QPVLTSQQIE TIFFKVPELY EIHKEFYDGL FPRVQQWSHQ QRVGDLFQKL ASQLGVYRAF VDNYGVAMEM AEKCCQANAQ FAEISENLRA RSNKDAKDPT TKNSLETLLY KPVDRVTRST LVLHDLLKHT PASHPDHPLL QDALRISQNF LSSINEEITP RRQSMTVK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5N6R, Strand ID: A Detail

Release date

2017-03-19

Citation

Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase
Reckel, S., Gehin, C., Tardivon, D., Georgeon, S., Kukenshoner, T., Lohr, F., Koide, A., Buchner, L., Panjkovich, A., Reynaud, A., Pinho, S., Gerig, B., Svergun, D., Pojer, F., Guntert, P., Dotsch, V., Koide, S., Gavin, A.C., Hantschel, O.
Nat. Commun. (2017), 8, 2101-2101, PubMed 29235475 , DOI 10.1038/s41467-017-02313-6 , Abstract

Related entities 1. Breakpoint cluster region protein (E.C.2.7.11.1), : 1 : 1 : 2 : 225 entities Detail

Interaction partners 1. Breakpoint cluster region protein (E.C.2.7.11.1), : 46 interactors Detail

More details for 46 interactors identified by 23 citations

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker 900 Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

4 3D HNCO

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

5 3D HNCACB

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

6 3D HN(CA)HA

Instrument

Bruker 950 Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

7 3D 1H-13C NOESY

Instrument

Bruker 950 Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

8 3D CCH-TOCSY

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

9 3D 1H-15N NOESY

Instrument

Bruker 800 Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

10 3D HN(CA)CO

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

11 3D HN(CO)CACB

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

12 3D (H)CC(CO)NH-TOCSY

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

13 3D H(CCCO)NH-TOCSY

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

14 2D 1H-13C HSQC aromatic

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

15 2D 1H-13C HSQC aromatic

Instrument

Bruker 600 Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

16 2D 1H-1H COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

17 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 0.85 mM [U-13C; U-15N] DH, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DH	[U-13C; U-15N]		0.85 mM
2	Hepes	natural abundance		50 mM
3	NaCl	natural abundance		50 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34101_5n6r.nef
Input source #2: Coordindates	5n6r.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

---490-------500-------510-------520-------530-------540-------550-------560-------570-------580----
AMASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTSQQIETIFFKVPELYEIHKEFYDGLFPRVQQWSHQQRVGDLFQKL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AMASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTSQQIETIFFKVPELYEIHKEFYDGLFPRVQQWSHQQRVGDLFQKL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---590-------600-------610-------620-------630-------640-------650-------660-------670-------680----
ASQLGVYRAFVDNYGVAMEMAEKCCQANAQFAEISENLRARSNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDLLKHTPASHPDHPLLQDALRISQNF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ASQLGVYRAFVDNYGVAMEMAEKCCQANAQFAEISENLRARSNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDLLKHTPASHPDHPLLQDALRISQNF
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

---690-------700--
LSSINEEITPRRQSMTVK
||||||||||||||||||
LSSINEEITPRRQSMTVK
-------210--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	218	0	0	100.0

Content subtype: combined_34101_5n6r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	2604		100.0 (chain: A, length: 218)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	6308 (1)	noe	100.0 (chain: A, length: 218)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	358 (358)	.	91.7 (chain: A, length: 218)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 218, Sequence coverage: 100.0%

---490-------500-------510-------520-------530-------540-------550-------560-------570-------580----
AMASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTSQQIETIFFKVPELYEIHKEFYDGLFPRVQQWSHQQRVGDLFQKL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AMASELDLEKGLEMRKWVLSGILASEETYLSHLEALLLPMKPLKAAATTSQPVLTSQQIETIFFKVPELYEIHKEFYDGLFPRVQQWSHQQRVGDLFQKL

---590-------600-------610-------620-------630-------640-------650-------660-------670-------680----
ASQLGVYRAFVDNYGVAMEMAEKCCQANAQFAEISENLRARSNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDLLKHTPASHPDHPLLQDALRISQNF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ASQLGVYRAFVDNYGVAMEMAEKCCQANAQFAEISENLRARSNKDAKDPTTKNSLETLLYKPVDRVTRSTLVLHDLLKHTPASHPDHPLLQDALRISQNF

---690-------700--
LSSINEEITPRRQSMTVK
||||||||||||||||||
LSSINEEITPRRQSMTVK

Total number of assignments
- ¹H chemical shifts: 1386
- ¹³C chemical shifts: 1008
- ¹⁵N chemical shifts: 210

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
488	SER	HG	4.731
504	SER	HG	4.268
509	SER	HG	7.623
512	THR	HG1	4.351
513	TYR	HH	9.166
515	SER	HG	8.194
516	HIS	HD1	6.98
532	THR	HG1	4.195
533	THR	HG1	5.584
534	SER	HG	4.275
539	THR	HG1	7.658
540	SER	HG	4.728
545	THR	HG1	3.905
554	TYR	HH	8.869
557	HIS	HD1	7.7
561	TYR	HH	8.584
572	SER	HG	3.978
573	HIS	HD1	8.006
586	SER	HG	4.711
591	TYR	HH	7.62
608	CYS	HG	1.504
609	CYS	HG	1.683
619	SER	HG	4.109
626	SER	HG	4.733
634	THR	HG1	4.732
635	THR	HG1	4.732
638	SER	HG	4.732
641	THR	HG1	4.728
651	THR	HG1	0.978
653	SER	HG	5.466
654	THR	HG1	0.736
658	HIS	HD1	8.13
663	HIS	HD1	6.913
664	THR	HG1	4.728
667	SER	HG	4.736
668	HIS	HD1	8.265
671	HIS	HD1	6.616
681	SER	HG	4.52
686	SER	HG	7.24
687	SER	HG	7.878
693	THR	HG1	7.65
698	SER	HG	4.729
700	THR	HG1	4.732

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1355	1342	99.0
¹³C chemical shifts	1013	1008	99.5
¹⁵N chemical shifts	241	210	87.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	431	430	99.8
¹³C chemical shifts	436	435	99.8
¹⁵N chemical shifts	207	207	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	924	912	98.7
¹³C chemical shifts	577	573	99.3
¹⁵N chemical shifts	34	3	8.8

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	135	135	100.0
¹³C chemical shifts	135	135	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	90	89	98.9
¹³C chemical shifts	88	88	100.0
¹⁵N chemical shifts	2	2	100.0

Redox state of CYS
Peptide bond of PRO
Tautomeric state of HIS
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_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 218, Sequence coverage: 100.0%
- Total number of restraints: 6271
- Weight of restraints: 1.0 (6271)
- Potential type of restraints: upper-bound-parabolic (6271)
- Range of distance target values: 2.31, 8.94 (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: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 218, Sequence coverage: 91.7%
- Total number of restraints: 358
- Total number of restraints per polymer type: 358
- Weight of restraints: 1.0 (358)
- Potential type of restraints: square-well-parabolic (358)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Bcr-Abl, Dbl-homology, Signaling Protein, helical bundle, leukemia, transferase