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Found 1 Document (1.119 seconds)

BMRB: 15290

2JQQ

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

Authors

Cavanaugh, L.F., Chen, X., Pelczer, I., Rizo, J., Hughson, F.M.

Assembly

Cog2p monomer

Entity

1. Cog2p monomer (polymer, Thiol state: all free), 204 monomers, 23417.25 Da Detail

GSDSLIRDLS GLSQKMVQTL LEQIRSNYDD YLTFSNTYTD EENETLINLE KTQSDLQKFM TQLDHLIKDD ISNTQEIIKD VLEYLKKLDE IYGSLRNHSQ LTEALSLGKR LSKSLHEMCG IEPLEEEICS GLIEQLYKLI TASRRILESC ADSNSPYIHH LRNDYQDLLQ EFQISLKILT EKCLENPSSL QNLSLTLVSI IKTA

Formula weight

23417.25 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.6 %, Completeness: 91.1 %, Completeness (bb): 92.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.1 % (2213 of 2428)	90.8 % (1149 of 1266)	91.5 % (858 of 938)	92.0 % (206 of 224)
Backbone	92.0 % (1120 of 1218)	92.7 % (381 of 411)	90.8 % (550 of 606)	94.0 % (189 of 201)
Sidechain	90.8 % (1279 of 1408)	89.9 % (769 of 855)	93.0 % (493 of 530)	73.9 % (17 of 23)
Aromatic	96.5 % (110 of 114)	96.5 % (55 of 57)	96.5 % (55 of 57)
Methyl	94.6 % (244 of 258)	94.6 % (122 of 129)	94.6 % (122 of 129)

1. Cog2p

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details same as for sample 1, but with D2O as solvent system

#	Name	Isotope labeling	Concentration
6	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
7	TRIS	natural abundance	3 (±0.05) mM
8	EDTA	natural abundance	50 (±0.05) uM
9	sodium chloride	natural abundance	10 (±0.05) mM
10	sodium azide	natural abundance	0.0025 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details To determine stereospecificity of leucine side chains

#	Name	Isotope labeling	Concentration
11	Cog2p	[U-10% 13C; U-100% 15N]	1 (±0.05) mM
12	TRIS	natural abundance	3 (±0.05) mM
13	EDTA	natural abundance	50 (±0.05) uM
14	sodium chloride	natural abundance	10 (±0.05) mM
15	sodium azide	natural abundance	0.0025 (±0.05) %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.25146
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.10134

Referencing offset: -0.69 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.25146
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.10134

Referencing offset: -0.69 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.25146
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.10134

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.25146
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.10134

Referencing offset: -0.41 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JQQ, Strand ID: A Detail

Release date

2007-07-01

Citation

Structural analysis of conserved oligomeric Golgi complex subunit 2
Cavanaugh, L.F., Chen, X., Richardson, B.C., Ungar, D., Pelczer, I., Rizo, J., Hughson, F.M.
J. Biol. Chem. (2007), 282, 23418-23426, PubMed 17565980 , DOI 10.1074/jbc.M703716200 , Abstract

Related entities 1. Cog2p monomer, : 1 : 2 entities Detail

Interaction partners 1. Cog2p monomer, : 29 interactors Detail

More details for 29 interactors identified by 5 citations

Experiments performed 10 experiments Detail

1 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

2 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

4 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details same as for sample 1, but with D2O as solvent system

#	Name	Isotope labeling	Concentration
6	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
7	TRIS	natural abundance	3 (±0.05) mM
8	EDTA	natural abundance	50 (±0.05) uM
9	sodium chloride	natural abundance	10 (±0.05) mM
10	sodium azide	natural abundance	0.0025 %

5 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details Primary sample

#	Name	Isotope labeling	Concentration
1	Cog2p	[U-100% 13C; U-100% 15N]	1 (±0.05) mM
2	TRIS	natural abundance	3 (±0.05) mM
3	EDTA	natural abundance	50 (±0.05) uM
4	sodium chloride	natural abundance	10 (±0.05) mM
5	sodium azide	natural abundance	0.0025 %

10 2D 1H-13C CT-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details To determine stereospecificity of leucine side chains

#	Name	Isotope labeling	Concentration
11	Cog2p	[U-10% 13C; U-100% 15N]	1 (±0.05) mM
12	TRIS	natural abundance	3 (±0.05) mM
13	EDTA	natural abundance	50 (±0.05) uM
14	sodium chloride	natural abundance	10 (±0.05) mM
15	sodium azide	natural abundance	0.0025 (±0.05) %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15290_2jqq.nef
Input source #2: Coordindates	2jqq.cif
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	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-60-------70--------80--------90-------100-------110-------120-------130-------140-------150-------1
GSDSLIRDLSGLSQKMVQTLLEQIRSNYDDYLTFSNTYTDEENETLINLEKTQSDLQKFMTQLDHLIKDDISNTQEIIKDVLEYLKKLDEIYGSLRNHSQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSDSLIRDLSGLSQKMVQTLLEQIRSNYDDYLTFSNTYTDEENETLINLEKTQSDLQKFMTQLDHLIKDDISNTQEIIKDVLEYLKKLDEIYGSLRNHSQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

60-------170-------180-------190-------200-------210-------220-------230-------240-------250-------2
LTEALSLGKRLSKSLHEMCGIEPLEEEICSGLIEQLYKLITASRRILESCADSNSPYIHHLRNDYQDLLQEFQISLKILTEKCLENPSSLQNLSLTLVSI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LTEALSLGKRLSKSLHEMCGIEPLEEEICSGLIEQLYKLITASRRILESCADSNSPYIHHLRNDYQDLLQEFQISLKILTEKCLENPSSLQNLSLTLVSI
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

60--
IKTA
||||
IKTA
----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	204	0	0	100.0

Content subtype: combined_15290_2jqq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2196		94.1 (chain: A, length: 204)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	5062 (1)	noe	73.0 (chain: A, length: 204)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	194 (1)	hbond	59.3 (chain: A, length: 204)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	254 (254)	.	68.6 (chain: A, length: 204)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 204, Sequence coverage: 94.1%
- Total number of assignments
  - ¹H chemical shifts: 1145
  - ¹³C chemical shifts: 846
  - ¹⁵N chemical shifts: 205
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1266	1145	90.4
¹³C chemical shifts	938	846	90.2
¹⁵N chemical shifts	231	205	88.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	411	378	92.0
¹³C chemical shifts	408	356	87.3
¹⁵N chemical shifts	201	188	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	855	767	89.7
¹³C chemical shifts	530	490	92.5
¹⁵N chemical shifts	30	17	56.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	132	125	94.7
¹³C chemical shifts	132	125	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	57	55	96.5
¹³C chemical shifts	57	55	96.5

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 204, Sequence coverage: 73.0%
- Total number of restraints: 4758
- Weight of restraints: 1.0 (4758)
- Potential type of restraints: lower-bound-parabolic (2), square-well-parabolic (4756)
- Range of distance target values: 1.8, 4.4 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 204, Sequence coverage: 59.3%
  - Total number of restraints: 194
  - Weight of restraints: 1.0 (194)
  - Potential type of restraints: square-well-parabolic (194)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 204, Sequence coverage: 68.6%
- Total number of restraints: 254
- Total number of restraints per polymer type: 254
- Weight of restraints: 1.0 (254)
- Potential type of restraints: square-well-parabolic (254)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Cog2, COG2, COG complex, Golgi, vesicle tethering, vesicular transport, helical bundle, protein

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Found 1 Document (1.119 seconds)

BMRB: 15290

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Cog2p monomer, : 1 : 2 entities Detail

Interaction partners 1. Cog2p monomer, : 29 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail