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- PDB-2l76: Solution NMR structure of human NFATC2IP ubiquitin-like domain, N... -

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Basic information

Entry
Database: PDB / ID: 2l76
TitleSolution NMR structure of human NFATC2IP ubiquitin-like domain, NFATC2IP_244_338, NESG target HT65A/OCSP target hs00387_244_338/SGC-toronto
ComponentsNFATC2-interacting protein
KeywordsTRANSCRIPTION / ubiquitin-like domain / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


protein sumoylation / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
NFATC2-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Houliston, S. / Doherty, R. / Semesi, A. / Dhe-Paganon, S. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: Human NFATC2IP ubiquitin-like domains
Authors: Doherty, R. / Wu, B. / Yee, A. / Lemak, A. / Houliston, S. / Fares, C. / Srisalam, S. / Bulter, C. / Edwards, A.M. / Weigelt, J. / Dhe-Paganon, S. / Arrowsmith, C.H.
History
DepositionDec 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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: NFATC2-interacting protein


Theoretical massNumber of molelcules
Total (without water)10,3961
Polymers10,3961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NFATC2-interacting protein / 45 kDa NF-AT-interacting protein / 45 kDa NFAT-interacting protein / Nuclear factor of activated T- ...45 kDa NF-AT-interacting protein / 45 kDa NFAT-interacting protein / Nuclear factor of activated T-cells / cytoplasmic 2-interacting protein


Mass: 10396.112 Da / Num. of mol.: 1 / Fragment: sequence database residues 244-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2IP, NIP45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NCF5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11012D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] NFATC2IP_244_338, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor ...Contents: 0.5 mM [U-100% 13C; U-100% 15N] NFATC2IP_244_338, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNFATC2IP_244_338-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 uMzinc sulphate-41
10 mMDTT-5[U-100% 2H]1
0.01 %NaN3-61
10 mMbenzamidine-71
1 %inhibitor cocktail-81
0.5 mMNFATC2IP_244_338-9[U-100% 13C; U-100% 15N]2
10 mMTRIS-10[U-100% 2H]2
300 mMsodium chloride-112
10 uMzinc sulphate-122
10 mMDTT-13[U-100% 2H]2
0.01 %NaN3-142
10 mMbenzamidine-152
1 %inhibitor cocktail-162
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
Sparky3.95Goddarddata analysis
FMCGUI2.4Lemak, Arrowsmithchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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