BMRB Entry 27556

Name: NMR chemical shifts of horse heart cytochrome c bound to 1:1 (molar) TOCL/DOPC vesicles.
Published: 2019-03-07

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27556

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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 chemical shifts of horse heart cytochrome c bound to 1:1 (molar) TOCL/DOPC vesicles.

Deposition date:

2018-07-24

Original release date:

2019-03-07

Authors:

Li, Mingyue; Mandal, Abhishek; Tyurin, Vladimir; DeLucia, Maria; Ahn, Jinwoo; Kagan, Valerian; van der Wel, Patrick

Citation:

Citation: Li, Mingyue; Mandal, Abhishek; Tyurin, Vladimir; DeLucia, Maria; Ahn, Jinwoo; Kagan, Valerian; van der Wel, Patrick. "Surface-Binding to Cardiolipin Nanodomains Triggers Cytochrome c Pro-apoptotic Peroxidase Activity via Localized Dynamics." Structure 27, 806-815 (2019).
PubMed: 30879887

Assembly members:

Assembly members:
horse_heart_cytochrome_c, polymer, 104 residues, Formula weight is not available
PROTOPORPHYRIN IX CONTAINING FE, non-polymer, 616.487 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pETDuet

Entity Sequences (FASTA):

Entity Sequences (FASTA):
horse_heart_cytochrome_c: GDVEKGKKIFVQKCAQCHTV EKGGKHKTGPNLHGLFGRKT GQAPGFTYTDANKNKGITWK EETLMEYLENPKKYIPGTKM IFAGIKKKTEREDLIAYLKK ATNE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	152
15N chemical shifts	50

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	protein	1
2	ligand	2

Entities:

Entity 1, protein 104 residues - Formula weight is not available

1

GLY

ASP

VAL

GLU

LYS

GLY

LYS

ILE

PHE

2

VAL

GLN

LYS

CYS

ALA

GLN

CYS

HIS

THR

VAL

3

GLU

LYS

GLY

LYS

HIS

LYS

THR

GLY

PRO

4

ASN

LEU

HIS

GLY

LEU

PHE

GLY

ARG

LYS

THR

5

GLY

GLN

ALA

PRO

GLY

PHE

THR

TYR

THR

ASP

6

ALA

ASN

LYS

ASN

LYS

GLY

ILE

THR

TRP

LYS

7

GLU

THR

LEU

MET

GLU

TYR

LEU

GLU

ASN

8

PRO

LYS

TYR

ILE

PRO

GLY

THR

LYS

MET

9

ILE

PHE

ALA

GLY

ILE

LYS

THR

GLU

10

ARG

GLU

ASP

LEU

ILE

ALA

TYR

LEU

LYS

11

ALA

THR

ASN

GLU

Entity 2, ligand - C34 H32 Fe N4 O4 - 616.487 Da.

1

HEM

Samples:

ssNMR_sample: horse heart cytochrome c, [U-99% 13C; U-99% 15N], 30 uL

sample_conditions_1: pH: 7.4; pressure: 1 atm; temperature: 252 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DARR	ssNMR_sample	isotropic	sample_conditions_1
2D NCA	ssNMR_sample	isotropic	sample_conditions_1
3D NCACX	ssNMR_sample	isotropic	sample_conditions_1
3D NCOCX	ssNMR_sample	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker Avance 750 MHz

UNP	P00004
AlphaFold	P00004