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BMRB: 16012

2KA1

Solution NMR structure of BNIP3 transmembrane peptide dimer in detergent micelles

Authors

Sulistijo, E.S., MacKenzie, K.R.

Assembly

Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3

Entity

1. Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3 (polymer, Thiol state: not present), 35 monomers, 3786.553 × 2 Da Detail

GGIFSAEFLK VFLPSLLLSH LLAIGLGIYI GRRLT

Total weight

7573.106 Da

Max. entity weight

3786.553 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.1 %, Completeness (bb): 97.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.1 % (414 of 422)	97.7 % (210 of 215)	98.8 % (171 of 173)	97.1 % (33 of 34)
Backbone	97.1 % (202 of 208)	95.9 % (71 of 74)	98.0 % (98 of 100)	97.1 % (33 of 34)
Sidechain	99.2 % (242 of 244)	98.6 % (139 of 141)	100.0 % (103 of 103)
Aromatic	100.0 % (42 of 42)	100.0 % (21 of 21)	100.0 % (21 of 21)
Methyl	98.4 % (61 of 62)	96.8 % (30 of 31)	100.0 % (31 of 31)

1. Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3

GGIFSAEFLK VFLPSLLLSH LLAIGLGIYI GRRLT

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2KA1, Strand ID: A, B Detail

Release date

2009-05-19

Citation

Structural basis for dimerization of the BNIP3 transmembrane domain
Sulistijo, E.S., MacKenzie, K.R.
Biochemistry (2009), 48, 5106-5120, PubMed 19415897 , DOI 10.1021/bi802245u , Abstract

Related entities 1. Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3, : 1 : 5 : 4 : 12 entities Detail

Interaction partners 1. Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3, : 12 interactors Detail

More details for 12 interactors identified by 5 citations

Experiments performed 13 experiments Detail

1 3D CN-NOESY-HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

2 3D 15N-edited NOESY-HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

3 3D 13C-edited NOESY-HSQC optimized for aromatic carbon

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

4 half-filtered 3D CN-NOESY-HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

5 2D spin-echo difference CT HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

6 HNHA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

7 HNCA

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

8 CBCACONNH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

9 HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

10 H(C)CH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

11 (H)CCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

12 HBCBCGCDHD

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

13 HBCBCGCDCEHE

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Temperature 313 K, pH 5.1, Details 10mM phosphate buffer, 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	[U-100% 13C; U-100% 15N]		0.4 mM
2	Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3	natural abundance		0.6 mM
3	phosphate buffer	natural abundance		10 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16012_2ka1.nef
Input source #2: Coordindates	2ka1.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

----160-------170-------180--------
GGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLT
|||||||||||||||||||||||||||||||||||
GGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLT
--------10--------20--------30-----

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

----160-------170-------180--------
GGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLT
|||||||||||||||||||||||||||||||||||
GGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLT
--------10--------20--------30-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0
B	B	35	0	0	100.0

Content subtype: combined_16012_2ka1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	439		100.0 (chain: A, length: 35)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2222 (1)	noe	100.0 (chain: A, length: 35), 100.0 (chain: B, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%

----160-------170-------180--------
GGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLT
|||||||||||||||||||||||||||||||||||
GGIFSAEFLKVFLPSLLLSHLLAIGLGIYIGRRLT

Total number of assignments
- ¹H chemical shifts: 222
- ¹³C chemical shifts: 178
- ¹⁵N chemical shifts: 39

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
157	PHE	CG	138.6
161	PHE	CG	139.1
165	PHE	CG	138.1
173	HIS	CG	128.0
182	TYR	CG	128.3
185	ARG	HH11	6.86
185	ARG	HH12	6.86
185	ARG	HH21	6.86
185	ARG	HH22	6.86
185	ARG	CZ	159.47
185	ARG	NH1	72.2
185	ARG	NH2	72.2
186	ARG	HH11	6.83
186	ARG	HH12	6.83
186	ARG	HH21	6.83
186	ARG	HH22	6.83
186	ARG	CZ	159.16
186	ARG	NH1	72.2
186	ARG	NH2	72.2

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	215	214	99.5
¹³C chemical shifts	173	171	98.8
¹⁵N chemical shifts	36	35	97.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	73	98.6
¹³C chemical shifts	70	68	97.1
¹⁵N chemical shifts	34	33	97.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	141	141	100.0
¹³C chemical shifts	103	103	100.0
¹⁵N chemical shifts	2	2	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	31	100.0
¹³C chemical shifts	31	31	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0
¹³C chemical shifts	21	21	100.0

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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 35, Sequence coverage: 100.0%
- Total number of restraints: 2216
- Weight of restraints: 1.0 (2216)
- Potential type of restraints: square-well-parabolic (2216)
- Range of distance target values: 1.65, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords bnip3, homodimer, integral membrane protein, membrane helix-helix interactions, membrane protein folding, transmembrane domain