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- PDB-1x2l: Solution structure of the CUT domain of human homeobox protein Cu... -

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Basic information

Entry
Database: PDB / ID: 1x2l
TitleSolution structure of the CUT domain of human homeobox protein Cux-2 (Cut-like 2)
ComponentsHomeobox protein Cux-2
KeywordsTRANSCRIPTION / CUT domain / human homeobox protein Cux-2 / Cut-like 2 / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of dendritic spine morphogenesis / short-term memory / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / cellular response to organic substance / positive regulation of excitatory postsynaptic potential / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding ...positive regulation of dendritic spine morphogenesis / short-term memory / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / cellular response to organic substance / positive regulation of excitatory postsynaptic potential / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleus
Similarity search - Function
CUT domain / CUT domain / CUT domain profile. / CUT / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain ...CUT domain / CUT domain / CUT domain profile. / CUT / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein cut-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKamatari, Y.O. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the CUT domain of human homeobox protein Cux-2 (Cut-like 2)
Authors: Kamatari, Y.O. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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: Homeobox protein Cux-2


Theoretical massNumber of molelcules
Total (without water)10,9481
Polymers10,9481
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 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Homeobox protein Cux-2 / / Cut-like 2


Mass: 10948.424 Da / Num. of mol.: 1 / Fragment: CUT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: CUTL2 / Plasmid: P040531-01 / References: UniProt: O14529

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.19mM CUT domain U-13C, 15N; 20mM d-Tris-HCl buffer (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA1.07Guntert, P.structure solution
OPALp1.2KORADI, R., BILLETER, M., GUNTERT, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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