BMRBj - BMREntryMaster

Found 1 Document (0.49 seconds)

BMRB: 34522

6ZDB

NMR structural analysis of yeast Cox13 reveals its C-terminus in interaction with ATP

Authors

Shu, Z., Pontus, P., Peter, B., Lena, M., Pia, A.

Assembly

Cytochrome c oxidase subunit 13, mitochondrial

Entity

1. Cytochrome c oxidase subunit 13, mitochondrial (polymer), 129 monomers, 15020.93 × 2 Da Detail

MFRQCAKRYA SSLPPNALKP AFGPPDKVAA QKFKESLMAT EKHAKDTSNM WVKISVWVAL PAIALTAVNT YFVEKEHAEH REHLKHVPDS EWPRDYEFMN IRSKPFFWGD GDKTLFWNPV VNRHIEHDD

Total weight

30041.86 Da

Max. entity weight

15020.93 Da

Source organism

Saccharomyces cerevisiae S288C

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.7 %, Completeness: 58.6 %, Completeness (bb): 85.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	58.6 % (924 of 1576)	51.7 % (424 of 820)	63.9 % (395 of 618)	76.1 % (105 of 138)
Backbone	85.5 % (645 of 754)	83.3 % (209 of 251)	86.2 % (331 of 384)	88.2 % (105 of 119)
Sidechain	41.4 % (392 of 948)	38.0 % (216 of 569)	48.9 % (176 of 360)	0.0 % (0 of 19)
Aromatic	9.9 % (19 of 192)	19.8 % (19 of 96)	0.0 % (0 of 91)	0.0 % (0 of 5)
Methyl	81.0 % (94 of 116)	81.0 % (47 of 58)	81.0 % (47 of 58)

1. entity 1

MFRQCAKRYA SSLPPNALKP AFGPPDKVAA QKFKESLMAT EKHAKDTSNM WVKISVWVAL PAIALTAVNT YFVEKEHAEH REHLKHVPDS EWPRDYEFMN IRSKPFFWGD GDKTLFWNPV VNRHIEHDD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313.15 K, pH 6.5, Details 0.5 mM [U-15N] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Cytochrome c oxidase subunit 13, Cox13	[U-15N]		0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313.15 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	Cytochrome c oxidase subunit 13, Cox13	[U-13C; U-15N]		0.5 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313.15 K, pH 6.5, Details 0.5 mM 50%[15N, 13C] mixed with 50% [14N, 12C] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Cytochrome c oxidase subunit 13, Cox13	50%[15N, 13C] mixed with 50% [14N, 12C]		0.5 mM

Release date

2020-07-13

Citation

NMR structural analysis of the yeast cytochrome c oxidase subunit Cox13 and its interaction with ATP
Zhou, S., Pettersson, P., Bjorck, M.L., Dawitz, H., Brzezinski, P., Maler, L., Adelroth, P.
BMC Biol. (2021), 19, 98-98, PubMed 33971868 , DOI 10.1186/s12915-021-01036-x , Abstract

Related entities 1. Cytochrome c oxidase subunit 13, mitochondrial, : 1 : 5 : 6 : 6 entities Detail

Interaction partners 1. Cytochrome c oxidase subunit 13, mitochondrial, : 6 interactors Detail

More details for 6 interactors identified by 4 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N TROSY HSQC

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313.15 K, pH 6.5, Details 0.5 mM [U-15N] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Cytochrome c oxidase subunit 13, Cox13	[U-15N]		0.5 mM

2 3D backbone experiments

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313.15 K, pH 6.5, Details 0.5 mM [U-13C; U-15N] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
2	Cytochrome c oxidase subunit 13, Cox13	[U-13C; U-15N]		0.5 mM

3 3D sidechain experiments

Instrument

Bruker AVANCE - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Cytochrome c oxidase subunit 13, Cox13	[U-13C; U-15N]		0.5 mM

4 3D 15N-NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Cytochrome c oxidase subunit 13, Cox13	[U-13C; U-15N]		0.5 mM

5 3D 13C-NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
2	Cytochrome c oxidase subunit 13, Cox13	[U-13C; U-15N]		0.5 mM

6 3D 15N-filtered/edited-NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313.15 K, pH 6.5, Details 0.5 mM 50%[15N, 13C] mixed with 50% [14N, 12C] Cytochrome c oxidase subunit 13, Cox13, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
3	Cytochrome c oxidase subunit 13, Cox13	50%[15N, 13C] mixed with 50% [14N, 12C]		0.5 mM

7 3D 13C-filtered/edited-NOESY

Instrument

Bruker AVANCE - 900 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
3	Cytochrome c oxidase subunit 13, Cox13	50%[15N, 13C] mixed with 50% [14N, 12C]		0.5 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34522_3.str
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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34522_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	962		90.7 (chain: 1, length: 129)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 129, Sequence coverage: 90.7%
- Total number of assignments
  - ¹H chemical shifts: 488
  - ¹³C chemical shifts: 373
  - ¹⁵N chemical shifts: 101
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	820	394	48.0
¹³C chemical shifts	618	373	60.4
¹⁵N chemical shifts	138	101	73.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	251	207	82.5
¹³C chemical shifts	258	215	83.3
¹⁵N chemical shifts	119	101	84.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	569	187	32.9
¹³C chemical shifts	360	158	43.9
¹⁵N chemical shifts	19	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	47	75.8
¹³C chemical shifts	62	47	75.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	19	19.8
¹³C chemical shifts	91	0	0.0
¹⁵N chemical shifts	5	0	0.0

Keywords ATP/ADP, STRUCTURAL PROTEIN, membrane protein, solution structure

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Found 1 Document (0.49 seconds)

BMRB: 34522

Sample #1

Sample #2

Sample #3

Related entities 1. Cytochrome c oxidase subunit 13, mitochondrial, : 1 : 5 : 6 : 6 entities Detail

Interaction partners 1. Cytochrome c oxidase subunit 13, mitochondrial, : 6 interactors Detail

Experiments performed 7 experiments Detail

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Chemical shift validation 3 contents Detail