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- PDB-1d5v: SOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTE-TRANSC... -

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Basic information

Entry
Database: PDB / ID: 1d5v
TitleSOLUTION STRUCTURE OF THE FORKHEAD DOMAIN OF THE ADIPOCYTE-TRANSCRIPTION FACTOR FREAC-11 (S12)
ComponentsS12 TRANSCRIPTION FACTOR (FKH-14)
KeywordsGENE REGULATION / WINGED HELIX / DNA-RECOGNITION HELIX
Function / homology
Function and homology information


apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / Formation of intermediate mesoderm / glomerular endothelium development / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / Formation of the ureteric bud / glomerular mesangial cell development / lymphangiogenesis ...apoptotic process involved in outflow tract morphogenesis / negative regulation of apoptotic process involved in outflow tract morphogenesis / paraxial mesodermal cell fate commitment / Formation of intermediate mesoderm / glomerular endothelium development / embryonic viscerocranium morphogenesis / positive regulation of vascular wound healing / Formation of the ureteric bud / glomerular mesangial cell development / lymphangiogenesis / podocyte differentiation / neural crest cell development / regulation of organ growth / metanephros development / camera-type eye development / embryonic heart tube development / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / negative regulation of cold-induced thermogenesis / artery morphogenesis / ureteric bud development / cardiac muscle cell proliferation / positive regulation of cell migration involved in sprouting angiogenesis / DNA-binding transcription activator activity / ventricular cardiac muscle tissue morphogenesis / branching involved in blood vessel morphogenesis / mesoderm development / blood vessel remodeling / anatomical structure morphogenesis / vascular endothelial growth factor receptor signaling pathway / somitogenesis / response to hormone / Notch signaling pathway / positive regulation of endothelial cell migration / ossification / blood vessel diameter maintenance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / chromatin DNA binding / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. ...: / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Forkhead box protein C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / COMBINED DISTANCE GEOMETRY, SIMULATING ANNEALING PROCEDURE
Authorsvan Dongen, M.J.P. / Cederberg, A. / Carlsson, P. / Enerback, S. / Wikstrom, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Solution structure and dynamics of the DNA-binding domain of the adipocyte-transcription factor FREAC-11.
Authors: van Dongen, M.J. / Cederberg, A. / Carlsson, P. / Enerback, S. / Wikstrom, M.
History
DepositionOct 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: S12 TRANSCRIPTION FACTOR (FKH-14)


Theoretical massNumber of molelcules
Total (without water)11,0841
Polymers11,0841
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)25 / 125structures with the lowest energy
RepresentativeModel #8closest to the average

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Components

#1: Protein S12 TRANSCRIPTION FACTOR (FKH-14)


Mass: 11083.717 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: ADIPOSE TISSUE / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99958

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1223D 13C-SEPARATED NOESY
131HNHA
141CROSS RELAXATION BETWEEN 13CA-1HA DIPOLAR AND 13C' CHEMICAL SHIFT ANISOTROPY
151CROSS RELAXATION BETWEEN 13CA-1HA AND 15N-1HN DIPOLAR INTERACTIONS
NMR detailsText: HNCA, HN(CO)CA, HNCACB, CACB(CO)NH AND HNCO EXPERIMENTS WERE USED TO OBTAIN SEQUENTIAL ASSIGNMENTS FOR THE BACKBONE. SIDE-CHAIN RESONANCES WERE ASSIGNED USING TOCSY-15N-HSQC, C(CO)NH, H(CCO)NH ...Text: HNCA, HN(CO)CA, HNCACB, CACB(CO)NH AND HNCO EXPERIMENTS WERE USED TO OBTAIN SEQUENTIAL ASSIGNMENTS FOR THE BACKBONE. SIDE-CHAIN RESONANCES WERE ASSIGNED USING TOCSY-15N-HSQC, C(CO)NH, H(CCO)NH AND HC(C)H-TOCSY EXPERIMENTS.

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Sample preparation

Details
Solution-IDContents
11 MM S12 DBD, 10 MM NACL, 5 MM MGCL2, 0.02% NAN3, 5 MM DTT
21 MM S12 DBD, 10 MM NACL, 5 MM MGCL2, 0.02% NAN3, 5 MM DTT
Sample conditionsIonic strength: 15 mM / pH: 6.1 / Pressure: AMBIENT / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS8001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian UNITYPLUSVarianUNITYPLUS5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1DELAGLIOrefinement
ANSIG3.3KRAULISrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: COMBINED DISTANCE GEOMETRY, SIMULATING ANNEALING PROCEDURE
Software ordinal: 1
Details: THE STRUCTURE WAS DETERMINED FROM 1042 DISTANCE RESTRAINTS, COMPLEMENTED WITH 145 RESTRAINTS ON DIHEDRAL ANGLES AND 36 RESTRAINTS ON HYDROGEN BOND LENGTHS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 25

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