BMRB Entry 15290

Name: Solution structure of Saccharomyces cerevisiae conserved oligomeric Golgi subunit 2 protein (Cog2p)
Published: 2007-07-02

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PDB ID: 2jqq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15290
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of Saccharomyces cerevisiae conserved oligomeric Golgi subunit 2 protein (Cog2p)

Deposition date:

2007-06-06

Original release date:

2007-07-02

Authors:

Cavanaugh, Lorraine; Chen, Xiaocheng; Pelczer, Istvan; Rizo, Josep; Hughson, Frederick

Citation:

Citation: Cavanaugh, Lorraine; Chen, Xiaocheng; Richardson, Brian; Ungar, Daniel; Pelczer, Istvan; Rizo, Josep; Hughson, Frederick. "Structural analysis of Conserved Oligomeric Golgi complex subunit 2" J. Biol. Chem. 282, 23418-23426 (2007).
PubMed: 17565980

Assembly members:

Assembly members:
Cog2p, polymer, 204 residues, 23454.13 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: pGEX-4T1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Cog2p: GSDSLIRDLSGLSQKMVQTL LEQIRSNYDDYLTFSNTYTD EENETLINLEKTQSDLQKFM TQLDHLIKDDISNTQEIIKD VLEYLKKLDEIYGSLRNHSQ LTEALSLGKRLSKSLHEMCG IEPLEEEICSGLIEQLYKLI TASRRILESCADSNSPYIHH LRNDYQDLLQEFQISLKILT EKCLENPSSLQNLSLTLVSI IKTA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	846
15N chemical shifts	205
1H chemical shifts	1395

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Cog2p monomer	1

Entities:

Entity 1, Cog2p monomer 204 residues - 23454.13 Da.

Initial GS in sequence is remains of thrombin cleavage site. D3 is amino acid 61 in the native protein sequence.

1

GLY

SER

ASP

SER

LEU

ILE

ARG

ASP

LEU

SER

2

GLY

LEU

SER

GLN

LYS

MET

VAL

GLN

THR

LEU

3

LEU

GLU

GLN

ILE

ARG

SER

ASN

TYR

ASP

4

TYR

LEU

THR

PHE

SER

ASN

THR

TYR

THR

ASP

5

GLU

ASN

GLU

THR

LEU

ILE

ASN

LEU

GLU

6

LYS

THR

GLN

SER

ASP

LEU

GLN

LYS

PHE

MET

7

THR

GLN

LEU

ASP

HIS

LEU

ILE

LYS

ASP

8

ILE

SER

ASN

THR

GLN

GLU

ILE

LYS

ASP

9

VAL

LEU

GLU

TYR

LEU

LYS

LEU

ASP

GLU

10

ILE

TYR

GLY

SER

LEU

ARG

ASN

HIS

SER

GLN

11

LEU

THR

GLU

ALA

LEU

SER

LEU

GLY

LYS

ARG

12

LEU

SER

LYS

SER

LEU

HIS

GLU

MET

CYS

GLY

13

ILE

GLU

PRO

LEU

GLU

ILE

CYS

SER

14

GLY

LEU

ILE

GLU

GLN

LEU

TYR

LYS

LEU

ILE

15

THR

ALA

SER

ARG

ILE

LEU

GLU

SER

CYS

16

ALA

ASP

SER

ASN

SER

PRO

TYR

ILE

HIS

17

LEU

ARG

ASN

ASP

TYR

GLN

ASP

LEU

GLN

18

GLU

PHE

GLN

ILE

SER

LEU

LYS

ILE

LEU

THR

19

GLU

LYS

CYS

LEU

GLU

ASN

PRO

SER

LEU

20

GLN

ASN

LEU

SER

LEU

THR

LEU

VAL

SER

ILE

21

ILE

LYS

THR

ALA

Samples:

H2O_Sample: Cog2p, [U-100% 13C; U-100% 15N], 1 ± 0.05 mM; TRIS 3 ± 0.05 mM; EDTA 50 ± 0.05 uM; sodium chloride 10 ± 0.05 mM; sodium azide 0.0025%

D2O_Sample: Cog2p, [U-100% 13C; U-100% 15N], 1 ± 0.05 mM; TRIS 3 ± 0.05 mM; EDTA 50 ± 0.05 uM; sodium chloride 10 ± 0.05 mM; sodium azide 0.0025%

10%_13C: Cog2p, [U-10% 13C; U-100% 15N], 1 ± 0.05 mM; TRIS 3 ± 0.05 mM; EDTA 50 ± 0.05 uM; sodium chloride 10 ± 0.05 mM; sodium azide 0.0025 ± 0.05 %

sample_conditions_1: ionic strength: 0.01 M; pH: 7; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	H2O_Sample	isotropic	sample_conditions_1
3D HNCACB	H2O_Sample	isotropic	sample_conditions_1
3D CBCA(CO)NH	H2O_Sample	isotropic	sample_conditions_1
2D DQF-COSY	D2O_Sample	isotropic	sample_conditions_1
2D 1H-15N HSQC	H2O_Sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	H2O_Sample	isotropic	sample_conditions_1
3D C(CO)NH	H2O_Sample	isotropic	sample_conditions_1
3D 1H-15N NOESY	H2O_Sample	isotropic	sample_conditions_1
3D 1H-13C NOESY	H2O_Sample	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC	10%_13C	isotropic	sample_conditions_1

Software:

CNS v1.1, A Brunger, P Adams, M Clore, P Gros, M Nilges and R Read - refinement, structure solution

NMRPipe, F Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Bax - processing

AQUA, T Rullmann, JF Doreleijers and R Kaptein - refinement

NMRView, B Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

TALOS, G Cornilescu, F Delaglio and A Bax - geometry optimization

xwinnmr, Bruker Biospin - collection

ProcheckNMR, RA Laskowski and M MacArthur - refinement

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 750 MHz
Varian INOVA 600 MHz

PDB	2JQQ
DBJ	GAA23495
EMBL	CAA58155 CAA97130 CAY79877
GB	AJP38895 AJR76215 AJR76714 AJR77212 AJR77712
REF	NP_011635
SP	P53271
TPG	DAA08212
AlphaFold	P53271