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- PDB-2mgq: Structure of CEH37 Homeodomain -

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Basic information

Entry
Database: PDB / ID: 2mgq
TitleStructure of CEH37 Homeodomain
ComponentsHomeobox protein ceh-37
KeywordsDNA BINDING PROTEIN / Homeodomain / Telomere binding protein
Function / homology
Function and homology information


chromosome, telomeric region => GO:0000781 / neuron fate specification / olfactory behavior / double-stranded telomeric DNA binding / telomere capping / DNA binding, bending / telomeric DNA binding / telomere organization / telomere maintenance / chromosome, telomeric region ...chromosome, telomeric region => GO:0000781 / neuron fate specification / olfactory behavior / double-stranded telomeric DNA binding / telomere capping / DNA binding, bending / telomeric DNA binding / telomere organization / telomere maintenance / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II
Similarity search - Function
Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / '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 ceh-37
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsMoon, S. / Lee, W.
CitationJournal: To be Published
Title: Structure of CEH37 Homeodomain
Authors: Moon, S. / Lee, W.
History
DepositionNov 4, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: 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 / 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 / _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: Homeobox protein ceh-37


Theoretical massNumber of molelcules
Total (without water)8,5121
Polymers8,5121
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Homeobox protein ceh-37


Mass: 8511.657 Da / Num. of mol.: 1 / Fragment: Homeodomain, UNP RESIDUES 38-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ceh-37, C37E2.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93356

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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 HN(CA)CB
1413D HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] CEH-37 Homeodomain-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: CEH-37 Homeodomain-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionspH: 7.5 / Temperature: 283 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddardrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 1172 / NOE long range total count: 187 / NOE medium range total count: 310 / NOE sequential total count: 675
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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