BMRB Entry 15301

Name: Solution model of crosslinked complex of cytochrome c and adrenodoxin
Published: 2008-06-12

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PDB ID: 2jqr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR15301
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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:

Solution model of crosslinked complex of cytochrome c and adrenodoxin

Deposition date:

2007-06-12

Original release date:

2008-06-12

Authors:

Xu, Xingfu; Reinle, Wolfgang; Hannemann, Frank; Konarev, Peter; Svergun, Dmitri; Bernhardt, Rita; Ubbink, Marcellus

Citation:

Citation: Xu, Xingfu; Reinle, Wolfgang; Hannemann, Frank; Konarev, Peter; Svergun, Dmitri; Bernhardt, Rita; Ubbink, Marcellus. "Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy" J. Am. Chem. Soc. 130, 6395-6403 (2008).
PubMed: 18439013

Assembly members:

Assembly members:
Cytc, polymer, 108 residues, Formula weight is not available
Adx, polymer, 105 residues, Formula weight is not available
HEME C, non-polymer, 618.503 Da.
FE2/S2 (INORGANIC) CLUSTER, non-polymer, 175.820 Da.

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Cytc: TEFKAGSAKKGATLFKTRCL QCHTVEKGGPHKCGPNLHGI FGRHSGQAEGYSYTDANIKK NVLWDENNMSEYLTNPKKYI PGTKMAFGGLKKEKDRNDLI TYLKKATE
Adx: EDKITVHFINRDGETLTTKG KIGDSLLDVVVQNNLDIDGF GACEGTLACSTCHLIFEQHI FEKLEAITDEENDMLDCAYG LTDRSRLGCQISLTKAMDNM TVRVP

Data sets:

assigned_chemical_shifts
- Adx_oxidized_CL
- Cc_oxdized_CL

Data type	Count
15N chemical shifts	146
1H chemical shifts	146

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CcV28C	1
2	AdxL80C	2
3	HEME C	3
4	FE2/S2 (INORGANIC) CLUSTER	4

Entities:

Entity 1, CcV28C 108 residues - Formula weight is not available

Residues -4-0 represent a non-native tag

1

THR

GLU

PHE

LYS

ALA

GLY

SER

ALA

LYS

2

GLY

ALA

THR

LEU

PHE

LYS

THR

ARG

CYS

LEU

3

GLN

CYS

HIS

THR

VAL

GLU

LYS

GLY

PRO

4

HIS

LYS

CYS

GLY

PRO

ASN

LEU

HIS

GLY

ILE

5

PHE

GLY

ARG

HIS

SER

GLY

GLN

ALA

GLU

GLY

6

TYR

SER

TYR

THR

ASP

ALA

ASN

ILE

LYS

7

ASN

VAL

LEU

TRP

ASP

GLU

ASN

MET

SER

8

GLU

TYR

LEU

THR

ASN

PRO

LYS

TYR

ILE

9

PRO

GLY

THR

LYS

MET

ALA

PHE

GLY

LEU

10

LYS

GLU

LYS

ASP

ARG

ASN

ASP

LEU

ILE

11

THR

TYR

LEU

LYS

ALA

THR

GLU

Entity 2, AdxL80C 105 residues - Formula weight is not available

The first two residues have no coordinates in AYF

1

GLU

ASP

LYS

ILE

THR

VAL

HIS

PHE

ILE

ASN

2

ARG

ASP

GLY

GLU

THR

LEU

THR

LYS

GLY

3

LYS

ILE

GLY

ASP

SER

LEU

ASP

VAL

4

VAL

GLN

ASN

LEU

ASP

ILE

ASP

GLY

PHE

5

GLY

ALA

CYS

GLU

GLY

THR

LEU

ALA

CYS

SER

6

THR

CYS

HIS

LEU

ILE

PHE

GLU

GLN

HIS

ILE

7

PHE

GLU

LYS

LEU

GLU

ALA

ILE

THR

ASP

GLU

8

GLU

ASN

ASP

MET

LEU

ASP

CYS

ALA

TYR

GLY

9

LEU

THR

ASP

ARG

SER

ARG

LEU

GLY

CYS

GLN

10

ILE

SER

LEU

THR

LYS

ALA

MET

ASP

ASN

MET

11

THR

VAL

ARG

VAL

PRO

Entity 3, HEME C - C34 H34 Fe N4 O4 - 618.503 Da.

1

HEC

Entity 4, FE2/S2 (INORGANIC) CLUSTER - Fe2 S2 - 175.820 Da.

1

FES

Samples:

CcV28C_AdxL80C: CcV28C, [U-98% 15N], 0.2 – 0.6 mM; AdxL80C0.2 – 0.6 mM; potassium phosphate 20 mM

AdxL80C_CcV28C: AdxL80C, [U-98% 15N], 0.2 – 0.6 mM; CcV28C0.2 – 0.6 mM; potassium phosphate 20 mM

CcV28C: CcV28C, [U-98% 15N], 1.0 mM; DTT 5 mM; potassium phosphate 20 mM

AdxL80C: AdxL80C, [U-98% 15N], 0.5 – 0.8 mM; DTT 5 mM; potassium phosphate 20 mM

sample_conditions_1: pH: 7.4; pressure: 1 atm; temperature: 285 K

sample_conditions_2: ionic strength: 0.4 M; pH: 7.4; pressure: 1 atm; temperature: 301 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	CcV28C_AdxL80C	isotropic	sample_conditions_1
2D 1H-15N HSQC	AdxL80C_CcV28C	isotropic	sample_conditions_1
3D 1H-15N NOESY	CcV28C_AdxL80C	isotropic	sample_conditions_2
3D 1H-15N NOESY	AdxL80C_CcV28C	isotropic	sample_conditions_2
2D 1H-15N HSQC	CcV28C	isotropic	sample_conditions_1
2D 1H-15N HSQC	AdxL80C	isotropic	sample_conditions_1
3D 1H-15N NOESY	AdxL80C	isotropic	sample_conditions_1
3D 1H-15N TOCSY	AdxL80C	isotropic	sample_conditions_1

Software:

AZARA, Boucher - processing

ANSIG, Kraulis - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker DMX 600 MHz

PDB	1YCC 1CHH 1CHJ 1CRG 1CSU 1CSV 1CSW 1CSX 1CTY 1CTZ 1IRV 1IRW 1KYO 1LMS 1NMI 1S6V 1U74 1YCC 1YFC 1YIC 2B0Z 2B10 2B11 2B12 2BCN 2GB8 2HV4 2JQR 2JTI 2LIR 2LIT 2MHM 2N18 2ORL 2PCC 2YCC 3CX5 3TYI 4MU8 4N0K 4P4Q 4YE1 1AYF 1AYF 1CJE 1E6E 1L6U 1L6V 2BT6 2JQR
BMRB	131 17845 17846 17903 17904 19638 4566 7390
DBJ	GAA24396 BAA00362 BAA00363
EMBL	CAA24605 CAA89576 CAY80764
GB	AAA62856 AAA88751 AAB59344 AHY79034 AJP39735 AAA30357 AAA30358 AAB21264 AAI09850 ABQ13041
PRF	1409323A
REF	NP_012582 NP_851354 XP_005889885 XP_010861227
SP	P00044 P00257
TPG	DAA08835 DAA22428
AlphaFold	P00044 P00257