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- PDB-2lk2: Solution NMR structure of homeobox domain (171-248) of human home... -

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Basic information

Entry
Database: PDB / ID: 2lk2
TitleSolution NMR structure of homeobox domain (171-248) of human homeobox protein TGIF1, Northeast Structural Genomics Consortium Target HR4411B
ComponentsHomeobox protein TGIF1
KeywordsTRANSCRIPTION / NESG / Structural Genomics / Northeast Structural Genomics Consortium / PSI-Biology
Function / homology
Function and homology information


co-SMAD binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to growth factor stimulus / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...co-SMAD binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cellular response to growth factor stimulus / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Homeobox KN domain / Homeobox KN domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein TGIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Cort, J.R. / Shastry, R. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Yang, Y. / Ramelot, T.A. / Cort, J.R. / Shastry, R. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of homeobox domain (171-248) of human homeobox protein TGIF1, Northeast Structural Genomics Consortium Target HR4411B.
Authors: Yang, Y. / Ramelot, T.A. / Cort, J.R. / Shastry, R. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionSep 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: Homeobox protein TGIF1


Theoretical massNumber of molelcules
Total (without water)10,6881
Polymers10,6881
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)20 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Homeobox protein TGIF1 / 5'-TG-3'-interacting factor 1


Mass: 10688.159 Da / Num. of mol.: 1
Fragment: Homeobox TALE-type DNA binding domain residues 171-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGIF1, TGIF / Production host: Escherichia coli (E. coli) / References: UniProt: Q15583

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1432D 1H-15N HSQC
1532D 1H-13C HSQC
1622D 1H-13C HSQC-CT
1723D 1H-15N NOESY
1813D 1H-13C NOESY aliph
1913D HNCO
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D HNCA
11313D HN(CO)CA
11413D HBHA(CO)NH
11513D H(CCO)NH
11613D C(CCO)NH
11713D (H)CCH-COSY
11813D (H)CCH-TOCSY
11933D CCH-TOCSY
12034D CC-NOESY
12113D 1H-15N NOESY NUS

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Sample preparation

Details
Solution-IDContentsSolvent system
10.41 mM [U-100% 13C; U-100% 15N] homeobox domain (171-248) of human homeobox protein TGIF1, 20 mM ammonium acetate, 100 mM sodium chloride, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.36 mM [U-5% 13C; U-100% 15N] homeobox domain (171-248) of human homeobox protein TGIF1, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.41 mM [U-100% 13C; U-100% 15N] homeobox domain (171-248) of human homeobox protein TGIF1, 20 mM ammonium acetate, 100 mM sodium chloride, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.41 mMhomeobox domain (171-248) of human homeobox protein TGIF1-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
100 mMsodium chloride-31
0.02 %sodium azide-41
10 mMDTT-51
5 mMcalcium chloride-61
0.36 mMhomeobox domain (171-248) of human homeobox protein TGIF1-7[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-82
100 mMsodium chloride-92
10 mMDTT-102
0.02 %sodium azide-112
5 mMcalcium chloride-122
0.41 mMhomeobox domain (171-248) of human homeobox protein TGIF1-13[U-100% 13C; U-100% 15N]3
20 mMammonium acetate-143
100 mMsodium chloride-153
0.02 %sodium azide-163
10 mMDTT-173
5 mMcalcium chloride-183
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
ASDP1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.4(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, Markley, Assadi, and Eghbalniachemical shift autoassignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR_NIH_with_HBDBSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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