BMRB Entry 34522

Name: NMR structural analysis of yeast Cox13 reveals its C-terminus in interaction with ATP
Published: 2021-05-14

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PDB ID: 6zdb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34522
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2020-06-14

Original release date:

2021-05-14

Authors:

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

Citation:

Citation: Zhou, Shu; Pettersson, Pontus; Bjorck, Markus; Dawitz, Hannah; Brzezinski, Peter; Maler, Lena; Adelroth, Pia. "NMR structural analysis of the yeast cytochrome c oxidase subunit Cox13 and its interaction with ATP" BMC Biol. 19, 98-98 (2021).
PubMed: 33971868

Assembly members:

Assembly members:
entity_1, polymer, 129 residues, 15046.146 Da.

Natural source:

Natural source: Common Name: budding yeasts Taxonomy ID: 559292 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli K-12

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MFRQCAKRYASSLPPNALKP AFGPPDKVAAQKFKESLMAT EKHAKDTSNMWVKISVWVAL PAIALTAVNTYFVEKEHAEH REHLKHVPDSEWPRDYEFMN IRSKPFFWGDGDKTLFWNPV VNRHIEHDD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	373
15N chemical shifts	101
1H chemical shifts	488

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 129 residues - 15046.146 Da.

1

MET

PHE

ARG

GLN

CYS

ALA

LYS

ARG

TYR

ALA

2

SER

LEU

PRO

ASN

ALA

LEU

LYS

PRO

3

ALA

PHE

GLY

PRO

ASP

LYS

VAL

ALA

4

GLN

LYS

PHE

LYS

GLU

SER

LEU

MET

ALA

THR

5

GLU

LYS

HIS

ALA

LYS

ASP

THR

SER

ASN

MET

6

TRP

VAL

LYS

ILE

SER

VAL

TRP

VAL

ALA

LEU

7

PRO

ALA

ILE

ALA

LEU

THR

ALA

VAL

ASN

THR

8

TYR

PHE

VAL

GLU

LYS

GLU

HIS

ALA

GLU

HIS

9

ARG

GLU

HIS

LEU

LYS

HIS

VAL

PRO

ASP

SER

10

GLU

TRP

PRO

ARG

ASP

TYR

GLU

PHE

MET

ASN

11

ILE

ARG

SER

LYS

PRO

PHE

TRP

GLY

ASP

12

GLY

ASP

LYS

THR

LEU

PHE

TRP

ASN

PRO

VAL

13

VAL

ASN

ARG

HIS

ILE

GLU

HIS

ASP

Samples:

sample_1: Cytochrome c oxidase subunit 13, Cox13, [U-15N], 0.5 mM

sample_2: Cytochrome c oxidase subunit 13, Cox13, [U-13C; U-15N], 0.5 mM

sample_3: Cytochrome c oxidase subunit 13, Cox13, 50%[15N, 13C] mixed with 50% [14N, 12C], 0.5 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 313.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY HSQC	sample_1	isotropic	sample_conditions_1
3D backbone experiments	sample_2	isotropic	sample_conditions_1
3D sidechain experiments	sample_2	isotropic	sample_conditions_1
3D 15N-NOESY	sample_2	isotropic	sample_conditions_1
3D 13C-NOESY	sample_2	isotropic	sample_conditions_1
3D 15N-filtered/edited-NOESY	sample_3	isotropic	sample_conditions_1
3D 13C-filtered/edited-NOESY	sample_3	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

CcpNmr Analysis, CCPN - data analysis

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMR spectrometers:

Bruker AVANCE 800 MHz
Bruker AVANCE 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks