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- PDB-2k40: NMR structure of HESX-1 homeodomain double mutant R31L/E42L -

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Basic information

Entry
Database: PDB / ID: 2k40
TitleNMR structure of HESX-1 homeodomain double mutant R31L/E42L
ComponentsHomeobox expressed in ES cells 1
KeywordsDNA BINDING PROTEIN / THERMOSTABLE HOMEODOMAIN VARIANT / Developmental protein / Disease mutation / DNA-binding / Dwarfism / Homeobox / Nucleus / Polymorphism / Transcription / Transcription regulation
Function / homology
Function and homology information


nose development / leukemia inhibitory factor signaling pathway / otic vesicle formation / gonad development / pituitary gland development / forebrain morphogenesis / camera-type eye development / stem cell population maintenance / cellular response to cadmium ion / regulation of embryonic development ...nose development / leukemia inhibitory factor signaling pathway / otic vesicle formation / gonad development / pituitary gland development / forebrain morphogenesis / camera-type eye development / stem cell population maintenance / cellular response to cadmium ion / regulation of embryonic development / thyroid gland development / canonical Wnt signaling pathway / ERK1 and ERK2 cascade / RNA polymerase II transcription regulatory region sequence-specific DNA binding / stem cell differentiation / brain development / multicellular organism growth / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus
Similarity search - Function
Homeobox expressed in ES cells 1 / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...Homeobox expressed in ES cells 1 / 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 expressed in ES cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsSolution structure of the thermostable double mutant R31L/E42L of human HESX-1 homeodomain
AuthorsAsensio, J. / Torrado, M. / Gonzalez, C. / Bastida, A.
CitationJournal: To be Published
Title: The role of conserved salt-bridges on homeodomain stability
Authors: Asensio, J. / Torrado, M. / Gonzalez, C. / Bastida, A. / Corzana, F.
History
DepositionMay 26, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeobox expressed in ES cells 1


Theoretical massNumber of molelcules
Total (without water)8,1271
Polymers8,1271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Homeobox expressed in ES cells 1 / Homeobox protein ANF / hAnf


Mass: 8127.353 Da / Num. of mol.: 1
Fragment: DNA binding domain of Human transcription factor Hesx-I (UNP residues 108-174)
Mutation: R31L, E42L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HESX1, HANF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBX0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: SOLUTION STRUCTURE OF THE THERMOSTABLE DOUBLE MUTANT R31L/E42L OF HUMAN HESX-1 HOMEODOMAIN
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1312D 1H-1H TOCSY
1422D 1H-1H TOCSY
1512D DQF-COSY
1622D DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM HESX-I HOMEODOMAIN, 90% H2O/10% D2O90% H2O/10% D2O
20.600 mM HESX-I HOMEODOMAIN, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.6 mMHESX-I HOMEODOMAIN1
0.600 mMHESX-I HOMEODOMAIN2
Sample conditionsIonic strength: 0.1 NaCl / pH: 6 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian UnityVarianUNITY5003

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Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
DYANAGuntert, Braun and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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