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- PDB-2l5g: Co-ordinates and 1H, 13C and 15N chemical shift assignments for t... -

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Basic information

Entry
Database: PDB / ID: 2l5g
TitleCo-ordinates and 1H, 13C and 15N chemical shift assignments for the complex of GPS2 53-90 and SMRT 167-207
Components
  • G protein pathway suppressor 2
  • Putative uncharacterized protein NCOR2
KeywordsTRANSCRIPTION REGULATOR / GPS2 / SMRT / TBL1 / co-repressor
Function / homology
Function and homology information


: / negative regulation of protein K63-linked ubiquitination / negative regulation of B cell receptor signaling pathway / Loss of MECP2 binding ability to the NCoR/SMRT complex / positive regulation of peroxisome proliferator activated receptor signaling pathway / response to mitochondrial depolarisation / GTPase inhibitor activity / negative regulation of toll-like receptor signaling pathway / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process ...: / negative regulation of protein K63-linked ubiquitination / negative regulation of B cell receptor signaling pathway / Loss of MECP2 binding ability to the NCoR/SMRT complex / positive regulation of peroxisome proliferator activated receptor signaling pathway / response to mitochondrial depolarisation / GTPase inhibitor activity / negative regulation of toll-like receptor signaling pathway / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / negative regulation of JNK cascade / Notch binding / regulation of fat cell differentiation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fat cell differentiation / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / regulation of lipid metabolic process / negative regulation of tumor necrosis factor-mediated signaling pathway / estrous cycle / positive regulation of cholesterol efflux / nuclear retinoid X receptor binding / JNK cascade / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / lactation / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / viral process / cyclin binding / cerebellum development / B cell differentiation / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / histone deacetylase binding / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / transcription corepressor activity / response to estradiol / transcription coactivator activity / nuclear body / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
G protein pathway suppressor 2 / G-protein pathway suppressor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...G protein pathway suppressor 2 / G-protein pathway suppressor / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Homeobox-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor corepressor 2 / G protein pathway suppressor 2 / G protein pathway suppressor 2 / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsGPS2/SMRT complex
AuthorsOberoi, J. / Yang, J. / Neuhaus, D. / Schwabe, J.W.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery.
Authors: Oberoi, J. / Fairall, L. / Watson, P.J. / Yang, J.C. / Czimmerer, Z. / Kampmann, T. / Goult, B.T. / Greenwood, J.A. / Gooch, J.T. / Kallenberger, B.C. / Nagy, L. / Neuhaus, D. / Schwabe, J.W.
History
DepositionNov 1, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G protein pathway suppressor 2
B: Putative uncharacterized protein NCOR2


Theoretical massNumber of molelcules
Total (without water)9,6412
Polymers9,6412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide G protein pathway suppressor 2 / GPS2 protein


Mass: 4692.491 Da / Num. of mol.: 1 / Fragment: UNP Residues 53-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: GPS2 / Plasmid: pET13a / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6FHM8, UniProt: Q13227*PLUS
#2: Protein/peptide Putative uncharacterized protein NCOR2


Mass: 4948.668 Da / Num. of mol.: 1 / Fragment: UNP Residues 167-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: NCOR2 / Plasmid: pET41 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C9JQE8, UniProt: Q9Y618*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: GPS2/SMRT complex
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC CT aliphatic
1412D 1H-13C HSQC CT aromatic
1512D 1H-1H NOESY
1612D 1H-1H NOESY (filtered to remove 15N-coupled signals in F1 and F2)
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D (H)CCH-COSY
11213D CCH-TOCSY
11313D C(CO)NH
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic
11613D 1H-13C NOESY aromatic
11722D 1H-15N HSQC
11822D 1H-13C HSQC
11922D 1H-13C HSQC aliphatic
12022D 1H-1H NOESY filtered to retain only interchain cross-peaks
12132D 1H-15N HSQC
12232D 1H-13C HSQC
12332D 1H-13C HSQC aliphatic
12432D 1H-1H NOESY filtered to retain only interchain cross-peaks
12513D HNHAHB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-98% 13C; U-98% 15N] GPS2_53-90, 0.4 mM [U-98% 13C; U-98% 15N] SMRT_167-207, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-98% 13C; U-98% 15N] SMRT_167-207, 0.4 mM GPS2_53-90, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-98% 13C; U-98% 15N] GPS2_53-90, 0.4 mM SMRT_167-207, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMGPS2_53-90[U-98% 13C; U-98% 15N]1
0.4 mMSMRT_167-207[U-98% 13C; U-98% 15N]1
0.4 mMSMRT_167-207[U-98% 13C; U-98% 15N]2
0.4 mMGPS2_53-902
0.4 mMGPS2_53-90[U-98% 13C; U-98% 15N]3
0.4 mMSMRT_167-2073
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
XwinNMR3.6Bruker Biospinprocessing
Analysis1.0.15CCPNdata analysis
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: xplor-nih
NMR constraintsNOE constraints total: 808 / NOE intraresidue total count: 177 / NOE long range total count: 139 / NOE medium range total count: 325 / NOE sequential total count: 167
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 35 / Maximum upper distance constraint violation: 0.203 Å
NMR ensemble rmsDistance rms dev: 0.077 Å / Distance rms dev error: 0.033 Å

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