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- PDB-2llk: Solution NMR structure of the N-terminal myb-like 1 domain of the... -

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Basic information

Entry
Database: PDB / ID: 2llk
TitleSolution NMR structure of the N-terminal myb-like 1 domain of the human cyclin-D-binding transcription factor 1 (hDMP1), Northeast Structural Genomics Consortium (NESG) target ID hr8011a
ComponentsCyclin-D-binding Myb-like transcription factor 1
KeywordsCELL CYCLE / TRANSCRIPTION / helix bundle / SGC / Structural Genomics Consortium / NESG / Northeast Structural Genomics Consortium / PSI-Biology
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Cyclin-D-binding Myb-like transcription factor 1, N-terminal / Cyclin-D-binding Myb-like transcription factor 1 N-terminal / : / Myb-like domain profile. / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like ...Cyclin-D-binding Myb-like transcription factor 1, N-terminal / Cyclin-D-binding Myb-like transcription factor 1 N-terminal / : / Myb-like domain profile. / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclin-D-binding Myb-like transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailsfewest violations, model 1
AuthorsMontecchio, M. / Lemak, A. / Yee, A. / Xu, C. / Garcia, M. / Houliston, S. / Min, J. / Bellanda, M. / Montelione, G.T. / Arrowsmith, C. ...Montecchio, M. / Lemak, A. / Yee, A. / Xu, C. / Garcia, M. / Houliston, S. / Min, J. / Bellanda, M. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG) / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Solution NMR structure of the N-terminal myb-like 1 domain of the human cyclin D binding transcription factor 1 (hDMP1).
Authors: Montecchio, M. / Lemak, A. / Yee, A. / Xu, C. / Garcia, M. / Houliston, S. / Min, J. / Bellanda, M. / Montelione, G.T. / Arrowsmith, C.
History
DepositionNov 10, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 23, 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

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Assembly

Deposited unit
A: Cyclin-D-binding Myb-like transcription factor 1


Theoretical massNumber of molelcules
Total (without water)8,3841
Polymers8,3841
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 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Cyclin-D-binding Myb-like transcription factor 1 / hDMTF1 / Cyclin-D-interacting Myb-like protein 1 / hDMP1


Mass: 8384.414 Da / Num. of mol.: 1 / Fragment: Myb-like 1 domain residues 220-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMTF1, DMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y222

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1712D 1H-13C HSQC aliphatic
1812D 1H-13C HSQC aromatic
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
11113D (H)CCH-TOCSY
11213D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] protein, 10 mM sodium phosphate, 400 mM NaCl, 0.01 mM ZnSO4, 10 mM DTT, 1 mM benzamidine, 0.01 % NaN3, 95 % H2O, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity 1-1[U-13C; U-15N]1
10 mMsodium phosphate-21
400 mMNaCl-31
0.01 mMZnSO4-41
10 mMDTT-51
1 mMbenzamidine-61
0.01 %NaN3-71
95 %H2O-81
5 %D2O-91
Sample conditionsIonic strength: 400 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardpeak picking
MDDGUIGutmanas A., Orekhov V.processing
FMCGUILemak A., Steren C., Llinas M., Arrowsmith C.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVSBhattacharya and Montelionestructure validation
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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