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- PDB-2jqq: Solution structure of Saccharomyces cerevisiae conserved oligomer... -

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Basic information

Entry
Database: PDB / ID: 2jqq
TitleSolution structure of Saccharomyces cerevisiae conserved oligomeric Golgi subunit 2 protein (Cog2p)
ComponentsConserved oligomeric Golgi complex subunit 2
KeywordsPROTEIN TRANSPORT / protein / helical bundle / vesicular transport / tethering
Function / homology
Function and homology information


retrograde transport, vesicle recycling within Golgi / autophagy of peroxisome / Golgi transport complex / cytoplasm to vacuole targeting by the Cvt pathway / intra-Golgi vesicle-mediated transport / extrinsic component of membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / macroautophagy / Golgi membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1240 / Conserved oligomeric Golgi complex, subunit 2, N-terminal / COG (conserved oligomeric Golgi) complex component, COG2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Conserved oligomeric Golgi complex subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsCavanaugh, L.F. / Chen, X. / Pelczer, I. / Rizo, J. / Hughson, F.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural analysis of conserved oligomeric Golgi complex subunit 2
Authors: Cavanaugh, L.F. / Chen, X. / Richardson, B.C. / Ungar, D. / Pelczer, I. / Rizo, J. / Hughson, F.M.
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.6May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved oligomeric Golgi complex subunit 2


Theoretical massNumber of molelcules
Total (without water)23,4431
Polymers23,4431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Conserved oligomeric Golgi complex subunit 2 / / COG complex subunit 2 / Protein SEC35


Mass: 23442.502 Da / Num. of mol.: 1 / Fragment: residues 61-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: COG2, SEC35 / Production host: Escherichia coli (E. coli) / References: UniProt: P53271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HN(CA)CB
1313D CBCA(CO)NH
1422D DQF-COSY
1512D 1H-15N HSQC
1613D (H)CCH-TOCSY
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11032D 1H-13C CT-HSQC
NMR detailsText: Experiments collected at the EMSL at PNNL. Residues 59-108 were present in the Cog2 protein used in this NMR study; however a lack of long-range contacts prevented the inclusion of these ...Text: Experiments collected at the EMSL at PNNL. Residues 59-108 were present in the Cog2 protein used in this NMR study; however a lack of long-range contacts prevented the inclusion of these residues in the final models.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] Cog2p, 3 mM TRIS, 50 uM EDTA, 10 mM sodium chloride, 0.0025 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCog2p[U-100% 13C; U-100% 15N]1
3 mMTRIS1
50 uMEDTA1
10 mMsodium chloride1
0.0025 %sodium azide1
1 mMCog2p[U-100% 13C; U-100% 15N]2
3 mMTRIS2
50 uMEDTA2
10 mMsodium chloride2
0.0025 %sodium azide2
1 mMCog2p[U-100% 13C; U-100% 15N]3
3 mMTRIS3
50 uMEDTA3
10 mMsodium chloride3
0.0025 %sodium azide3
Sample conditionsIonic strength: 0.01 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A Brunger, P Adams, M Clore, P Gros, M Nilges and R Readstructure solution
CNS1.1A Brunger, P Adams, M Clore, P Gros, M Nilges and R Readrefinement
NMRPipeF Delaglio, S Grzesiek, GW Vuister, G Zhu, J Pfeifer and A Baxprocessing
AQUAT Rullmann, JF Doreleijers and R Kapteinrefinement
NMRViewB Johnson, One Moon Scientificpeak picking
NMRViewB Johnson, One Moon Scientificchemical shift assignment
NMRViewB Johnson, One Moon Scientificdata analysis
TALOSG Cornilescu, F Delaglio and A Baxgeometry optimization
XwinNMRBruker Biospincollection
ProcheckNMRRA Laskowski and M MacArthurrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1200 / Conformers submitted total number: 20

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