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BMRB: 18340

2LR1

Structural Mechanism for Bax Inhibition by Cytomegalovirus Protein vMIA

Authors

Assembly

Bax+vMIA

Entity

1. Bax+vMIA, entity 1 (polymer), 192 monomers, 21184.17 Da Detail

MDGSGEQPRG GGPTSSEQIM KTGALLLQGF IQDRAGRMGG EAPELALDPV PQDASTKKLS ECLKRIGDEL DSNMELQRMI AAVDTDSPRE VFFRVAADMF SDGNFNWGRV VALFYFASKL VLKALCTKVP ELIRTIMGWT LDFLRERLLG WIQDQGGWDG LLSYFGTPTW QTVTIFVAGV LTASLTIWKK MG

2. Bax+vMIA, entity 2 (polymer), 21 monomers, 2723.216 Da Detail

CEALKKALRR HRFLWQRRQR A

Total weight

23907.387 Da

Max. entity weight

21184.17 Da

Source organism

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 12.2 %, Completeness: 7.0 %, Completeness (bb): 7.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	7.0 % (176 of 2507)	8.7 % (113 of 1305)	4.9 % (48 of 976)	6.6 % (15 of 226)
Backbone	7.1 % (90 of 1262)	10.3 % (45 of 439)	4.9 % (30 of 618)	7.3 % (15 of 205)
Sidechain	7.0 % (101 of 1437)	7.9 % (68 of 866)	6.0 % (33 of 550)	0.0 % (0 of 21)
Aromatic	1.9 % (4 of 214)	1.9 % (2 of 107)	2.0 % (2 of 100)	0.0 % (0 of 7)
Methyl	9.2 % (22 of 240)	8.3 % (10 of 120)	10.0 % (12 of 120)

1. entity 1

MDGSGEQPRG GGPTSSEQIM KTGALLLQGF IQDRAGRMGG EAPELALDPV PQDASTKKLS ECLKRIGDEL DSNMELQRMI AAVDTDSPRE VFFRVAADMF SDGNFNWGRV VALFYFASKL VLKALCTKVP ELIRTIMGWT LDFLRERLLG WIQDQGGWDG LLSYFGTPTW QTVTIFVAGV LTASLTIWKK MG

2. entity 2

CEALKKALRR HRFLWQRRQR A

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-100% 15N]		0.1 mM
8	entity_2	natural abundance		0.1 mM
9	potassium phosphate	natural abundance		20 mM
10	D2O	[U-100% 2H]		10 %
11	H2O	natural abundance		90 %
12	DTT	natural abundance		0 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2LR1, Strand ID: A, B Detail

Release date

2012-12-03

Citation

Structural mechanism of Bax inhibition by cytomegalovirus protein vMIA
Ma, J., Edlich, F., Bermejo, G.A., Norris, K.L., Youle, R.J., Tjandra, N.
Proc. Natl. Acad. Sci. U. S. A. (2012), 109, 20901-20906, PubMed 23213219 , DOI 10.1073/pnas.1217094110 , Abstract

Related entities 1. Bax+vMIA, entity 1, : 1 : 9 entities Detail

Related entities 2. Bax+vMIA, entity 2, : 1 : 1 entities Detail

Interaction partners 2. Bax+vMIA, entity 2, : 1 interactors Detail

More details for 1 interactors identified by 1 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 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-100% 15N]		0.1 mM
8	entity_2	natural abundance		0.1 mM
9	potassium phosphate	natural abundance		20 mM
10	D2O	[U-100% 2H]		10 %
11	H2O	natural abundance		90 %
12	DTT	natural abundance		0 mM

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

4 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

10 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	entity_1	natural abundance		0.1 mM
2	entity_2	[U-100% 13C; U-100% 15N]		0.1 mM
3	potassium phosphate	natural abundance		20 mM
4	D2O	[U-100% 2H]		10 %
5	H2O	natural abundance		90 %
6	DTT	natural abundance		0 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18340_2lr1.nef
Input source #2: Coordindates	2lr1.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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MDGSGEQPRGGGPTSSEQIMKTGALLLQGFIQDRAGRMGGEAPELALDPVPQDASTKKLSECLKRIGDELDSNMELQRMIAAVDTDSPREVFFRVAADMF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDGSGEQPRGGGPTSSEQIMKTGALLLQGFIQDRAGRMGGEAPELALDPVPQDASTKKLSECLKRIGDELDSNMELQRMIAAVDTDSPREVFFRVAADMF

-------110-------120-------130-------140-------150-------160-------170-------180-------190--
SDGNFNWGRVVALFYFASKLVLKALCTKVPELIRTIMGWTLDFLRERLLGWIQDQGGWDGLLSYFGTPTWQTVTIFVAGVLTASLTIWKKMG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SDGNFNWGRVVALFYFASKLVLKALCTKVPELIRTIMGWTLDFLRERLLGWIQDQGGWDGLLSYFGTPTWQTVTIFVAGVLTASLTIWKKMG

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

130-----140-------150
CEALKKALRRHRFLWQRRQRA
|||||||||||||||||||||
CEALKKALRRHRFLWQRRQRA
--------10--------20-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	192	0	0	100.0
B	B	21	0	0	100.0

Content subtype: combined_18340_2lr1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	155		95.2 (chain: B, length: 21)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	245 (1)	noe	95.2 (chain: B, length: 21)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 95.2%
- Total number of assignments
  - ¹H chemical shifts: 106
  - ¹³C chemical shifts: 38
  - ¹⁵N chemical shifts: 11
- Completeness of assignments
  - Entity_assemble_ID: B
- 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: B

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 95.2%
- Total number of restraints: 245
- Weight of restraints: 1.0 (245)
- Potential type of restraints: square-well-parabolic (245)
- Range of distance target values: 3.1, 4.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
- Distance restraints on contact map

Keywords Bax, vMIA