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BMRB: 19538

2MF7

SOLUTION STRUCTURE OF THE IMS DOMAIN OF THE MITOCHONDRIAL IMPORT PROTEIN TIM21 FROM S. CEREVISIAE

Authors

Bajaj, R., Jaremko, L., Jaremko, M., Becker, S., Zweckstetter, M.

Assembly

IMS DOMAIN OF THE MITOCHONDRIAL IMPORT PROTEIN TIM21 FROM S. CEREVISIAE

Entity

1. IMS DOMAIN OF THE MITOCHONDRIAL IMPORT PROTEIN TIM21 FROM S. CEREVISIAE (polymer), 127 monomers, 14733.76 Da Detail

GAMGSGDTQL FNRAVSMVEK NKDIRSLLQC DDGITGKERL KAYGELITND KWTRNRPIVS TKKLDKEGRT HHYMRFHVES KKKIALVHLE AKESKQNYQP DFINMYVDVP GEKRYYLIKP KLHPVSN

Formula weight

14733.76 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.6 %, Completeness (bb): 85.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (1401 of 1546)	97.3 % (796 of 818)	80.0 % (475 of 594)	97.0 % (130 of 134)
Backbone	85.1 % (640 of 752)	98.8 % (254 of 257)	71.8 % (268 of 373)	96.7 % (118 of 122)
Sidechain	96.5 % (881 of 913)	96.8 % (543 of 561)	95.9 % (326 of 340)	100.0 % (12 of 12)
Aromatic	78.2 % (86 of 110)	81.8 % (45 of 55)	74.1 % (40 of 54)	100.0 % (1 of 1)
Methyl	100.0 % (122 of 122)	100.0 % (61 of 61)	100.0 % (61 of 61)

1. entity

GAMGSGDTQL FNRAVSMVEK NKDIRSLLQC DDGITGKERL KAYGELITND KWTRNRPIVS TKKLDKEGRT HHYMRFHVES KKKIALVHLE AKESKQNYQP DFINMYVDVP GEKRYYLIKP KLHPVSN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.29 ppm, Outliers: 4 Detail

LACS Plot; CB

Referencing offset: 0.29 ppm, Outliers: 4 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MF7, Strand ID: A Detail

Release date

2014-04-13

Citation

Structure of the mitochondrial translocator protein in complex with a diagnostic ligand
Jaremko, L., Jaremko, M., Giller, K., Becker, S., Zweckstetter, M.
Science (2014), 343, 1363-1366, PubMed 24653034 , DOI 10.1126/science.1248725 , Abstract

Related entities 1. IMS DOMAIN OF THE MITOCHONDRIAL IMPORT PROTEIN TIM21 FROM S. CEREVISIAE, : 1 : 1 : 5 : 11 entities Detail

Interaction partners 1. IMS DOMAIN OF THE MITOCHONDRIAL IMPORT PROTEIN TIM21 FROM S. CEREVISIAE, : 16 interactors Detail

More details for 16 interactors identified by 6 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.3 ~ 0.8 mM
2	sodium chloride	natural abundance		50 mM
3	HEPES	natural abundance		20 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19538_2mf7.nef
Input source #2: Coordindates	2mf7.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
GAMGSGDTQLFNRAVSMVEKNKDIRSLLQCDDGITGKERLKAYGELITNDKWTRNRPIVSTKKLDKEGRTHHYMRFHVESKKKIALVHLEAKESKQNYQP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGSGDTQLFNRAVSMVEKNKDIRSLLQCDDGITGKERLKAYGELITNDKWTRNRPIVSTKKLDKEGRTHHYMRFHVESKKKIALVHLEAKESKQNYQP

-------110-------120-------
DFINMYVDVPGEKRYYLIKPKLHPVSN
|||||||||||||||||||||||||||
DFINMYVDVPGEKRYYLIKPKLHPVSN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_19538_2mf7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1372		100.0 (chain: A, length: 127)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3183 (1)	noe	99.2 (chain: A, length: 127)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	188 (188)	.	78.7 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 792
  - ¹³C chemical shifts: 451
  - ¹⁵N chemical shifts: 129
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 99.2%
- Total number of restraints: 3183
- Weight of restraints: 1.0 (3183)
- Potential type of restraints: square-well-parabolic (3183)
- Range of distance target values: 2.7, 4.2 (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: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 78.7%
- Total number of restraints: 188
- Total number of restraints per polymer type: 188
- Weight of restraints: 1.0 (188)
- Potential type of restraints: square-well-parabolic (188)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords IMS domain, membrane, mitochondria, mitochondrial import protein, translocation