BMRBj - BMREntryMaster

Found 1 Document (1.181 seconds)

BMRB: 19054

2M5I

NMR structures of human apoptotic protein tBid in LPPG micelle

Authors

Wang, Y., Suzuki, M., Tjandra, N.

Assembly

human apoptotic protein tBid

Entity

1. human apoptotic protein tBid (polymer, Thiol state: not present), 135 monomers, 15220.06 Da Detail

GNRSSHSRLG RIEADSESQE DIIRNIARHL AQVGDSMDRS IPPGLVNGLA LQLRNTSRSE EDRNRDLATA LEQLLQAYPR DMEKEKTMLV LALLLAKKVA SHTPSLLRDV FHTTVNFINQ NLRTYVRSLA RNGMD

Formula weight

15220.06 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.0 %, Completeness: 92.4 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.4 % (1433 of 1551)	90.8 % (737 of 812)	95.8 % (568 of 593)	87.7 % (128 of 146)
Backbone	95.5 % (766 of 802)	94.9 % (258 of 272)	95.7 % (382 of 399)	96.2 % (126 of 131)
Sidechain	90.3 % (793 of 878)	88.7 % (479 of 540)	96.6 % (312 of 323)	13.3 % (2 of 15)
Aromatic	76.9 % (40 of 52)	76.9 % (20 of 26)	76.9 % (20 of 26)
Methyl	100.0 % (164 of 164)	100.0 % (82 of 82)	100.0 % (82 of 82)

1. entity

GNRSSHSRLG RIEADSESQE DIIRNIARHL AQVGDSMDRS IPPGLVNGLA LQLRNTSRSE EDRNRDLATA LEQLLQAYPR DMEKEKTMLV LALLLAKKVA SHTPSLLRDV FHTTVNFINQ NLRTYVRSLA RNGMD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

Sample #2

Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
7	tBid in LPPG micelle	[U-100% 13C; U-100% 15N]	1.0 (±0.2) mM
8	D2O	natural abundance	100 %
9	Potassium Phosphate	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.3 ppm	na	indirect	0.2514495
¹H	DSS	methyl protons	0.02 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.2 ppm	na	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.3 ppm	na	indirect	0.2514495
¹H	DSS	methyl protons	0.02 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.2 ppm	na	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.3 ppm	na	indirect	0.2514495
¹H	DSS	methyl protons	0.02 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.2 ppm	na	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.3 ppm	na	indirect	0.2514495
¹H	DSS	methyl protons	0.02 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.2 ppm	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M5I, Strand ID: A Detail

Release date

2013-11-10

Citation

Structural insights of tBid, the caspase-8-activated Bid, and its BH3 domain
Wang, Y., Tjandra, N.
J. Biol. Chem. (2013), 288, 35840-35851, PubMed 24158446 , DOI 10.1074/jbc.M113.503680 , Abstract

Related entities 1. human apoptotic protein tBid, : 1 : 3 : 8 entities Detail

Interaction partners 1. human apoptotic protein tBid, : 38 interactors Detail

More details for 38 interactors identified by 15 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

8 4D HCHC-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
7	tBid in LPPG micelle	[U-100% 13C; U-100% 15N]	1.0 (±0.2) mM
8	D2O	natural abundance	100 %
9	Potassium Phosphate	natural abundance	50 mM

9 T1

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

10 T2

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 (±1) atm, Temperature 318 (±0.2) K, pH 6.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	tBid in LPPG micelle	[U-15N]	0.5 (±0.1) mM
2	tBid in LPPG micelle	[U-13C; U-15N]	0.8 (±0.2) mM
3	tBid in LPPG micelle	[U-100% 15N; U-80% 2H]	0.8 (±0.2) mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %
6	Potassium Phosphate	natural abundance	50 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19054_2m5i.nef
Input source #2: Coordindates	2m5i.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

--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160
GNRSSHSRLGRIEADSESQEDIIRNIARHLAQVGDSMDRSIPPGLVNGLALQLRNTSRSEEDRNRDLATALEQLLQAYPRDMEKEKTMLVLALLLAKKVA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GNRSSHSRLGRIEADSESQEDIIRNIARHLAQVGDSMDRSIPPGLVNGLALQLRNTSRSEEDRNRDLATALEQLLQAYPRDMEKEKTMLVLALLLAKKVA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------170-------180-------190-----
SHTPSLLRDVFHTTVNFINQNLRTYVRSLARNGMD
|||||||||||||||||||||||||||||||||||
SHTPSLLRDVFHTTVNFINQNLRTYVRSLARNGMD
-------110-------120-------130-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	135	0	0	100.0

Content subtype: combined_19054_2m5i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1426		96.3 (chain: A, length: 135)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2003 (1)	noe	95.6 (chain: A, length: 135)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	2 (1)	undefined	2.2 (chain: A, length: 135)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	80 (1)	hbond	45.2 (chain: A, length: 135)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	144 (144)	.	62.2 (chain: A, length: 135)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 737
  - ¹³C chemical shifts: 564
  - ¹⁵N chemical shifts: 125
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	812	737	90.8
¹³C chemical shifts	593	564	95.1
¹⁵N chemical shifts	161	125	77.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	272	260	95.6
¹³C chemical shifts	270	253	93.7
¹⁵N chemical shifts	131	125	95.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	540	477	88.3
¹³C chemical shifts	323	311	96.3
¹⁵N chemical shifts	30	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	86	100.0
¹³C chemical shifts	86	86	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	26	20	76.9
¹³C chemical shifts	26	20	76.9

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 95.6%
- Total number of restraints: 1937
- Weight of restraints: 1.0 (1937)
- Potential type of restraints: square-well-parabolic (1937)
- Range of distance target values: 1.9, 5.0 (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
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 2.2%
  - Total number of restraints: 2
  - Weight of restraints: 1.0 (2)
  - Potential type of restraints: square-well-parabolic (2)
  - Range of distance target values: 10.0, 10.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 45.2%
    - Total number of restraints: 80
    - Weight of restraints: 1.0 (80)
    - Potential type of restraints: square-well-parabolic (80)
    - Range of distance target values: 1.55, 2.55 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 62.2%
- Total number of restraints: 144
- Total number of restraints per polymer type: 144
- Weight of restraints: 1.0 (144)
- Potential type of restraints: square-well-parabolic (144)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords apoptosis, LPPG micelle, membrane protein, tBid

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 (1.181 seconds)

BMRB: 19054

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. human apoptotic protein tBid, : 1 : 3 : 8 entities Detail

Interaction partners 1. human apoptotic protein tBid, : 38 interactors Detail

Experiments performed 10 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail