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- PDB-2ql2: Crystal Structure of the basic-helix-loop-helix domains of the he... -

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Basic information

Entry
Database: PDB / ID: 2ql2
TitleCrystal Structure of the basic-helix-loop-helix domains of the heterodimer E47/NeuroD1 bound to DNA
Components
  • DNA (5'-D(*DAP*DGP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DTP*DGP*DGP*DCP*DCP*DTP*DA)-3')
  • DNA (5'-D(*DTP*DAP*DGP*DGP*DCP*DCP*DAP*DTP*DCP*DTP*DGP*DGP*DTP*DCP*DCP*DT)-3')
  • Neurogenic differentiation factor 1
  • Transcription factor E2-alpha
Keywordstranscription/DNA / basic-helix-loop-helix / protein-DNA complex / heterodimer / DNA-binding / Activator / Developmental protein / Differentiation / Neurogenesis / Nucleus / Phosphorylation / Transcription / Transcription regulation / Cytoplasm / Phosphoprotein / transcription-DNA COMPLEX
Function / homology
Function and homology information


pancreatic A cell fate commitment / pancreatic PP cell fate commitment / regulation of intestinal epithelial structure maintenance / negative regulation of type B pancreatic cell apoptotic process / enteroendocrine cell differentiation / amacrine cell differentiation / bHLH transcription factor binding / embryonic organ morphogenesis / cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs ...pancreatic A cell fate commitment / pancreatic PP cell fate commitment / regulation of intestinal epithelial structure maintenance / negative regulation of type B pancreatic cell apoptotic process / enteroendocrine cell differentiation / amacrine cell differentiation / bHLH transcription factor binding / embryonic organ morphogenesis / cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / lymphocyte differentiation / natural killer cell differentiation / hindbrain development / endocrine pancreas development / immunoglobulin V(D)J recombination / Peyer's patch development / Myogenesis / dentate gyrus development / negative regulation of receptor signaling pathway via JAK-STAT / camera-type eye development / regulation of neuron differentiation / signal transduction involved in regulation of gene expression / anterior/posterior pattern specification / insulin secretion / B cell lineage commitment / E-box binding / inner ear development / regulation of G1/S transition of mitotic cell cycle / cell fate commitment / cell surface receptor signaling pathway via JAK-STAT / response to glucose / positive regulation of DNA-binding transcription factor activity / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / gastrulation / positive regulation of B cell proliferation / positive regulation of neuron differentiation / cerebellum development / erythrocyte differentiation / positive regulation of cell differentiation / RNA polymerase II transcription regulator complex / nervous system development / glucose homeostasis / nucleosome / T cell differentiation in thymus / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / transcription regulator complex / gene expression / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / response to xenobiotic stimulus / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Neurogenic differentiation factor NeuroD / Neurogenic differentiation factor, domain of unknown function / : / Neuronal helix-loop-helix transcription factor / : / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...Neurogenic differentiation factor NeuroD / Neurogenic differentiation factor, domain of unknown function / : / Neuronal helix-loop-helix transcription factor / : / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor E2-alpha / Neurogenic differentiation factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRose, R.B. / Longo, A. / Guanga, G.P.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure of E47-NeuroD1/beta2 bHLH domain-DNA complex: heterodimer selectivity and DNA recognition.
Authors: Longo, A. / Guanga, G.P. / Rose, R.B.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor E2-alpha
B: Neurogenic differentiation factor 1
C: Transcription factor E2-alpha
D: Neurogenic differentiation factor 1
E: DNA (5'-D(*DTP*DAP*DGP*DGP*DCP*DCP*DAP*DTP*DCP*DTP*DGP*DGP*DTP*DCP*DCP*DT)-3')
F: DNA (5'-D(*DAP*DGP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DTP*DGP*DGP*DCP*DCP*DTP*DA)-3')
G: DNA (5'-D(*DTP*DAP*DGP*DGP*DCP*DCP*DAP*DTP*DCP*DTP*DGP*DGP*DTP*DCP*DCP*DT)-3')
H: DNA (5'-D(*DAP*DGP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DTP*DGP*DGP*DCP*DCP*DTP*DA)-3')


Theoretical massNumber of molelcules
Total (without water)47,8508
Polymers47,8508
Non-polymers00
Water73941
1
A: Transcription factor E2-alpha
B: Neurogenic differentiation factor 1
E: DNA (5'-D(*DTP*DAP*DGP*DGP*DCP*DCP*DAP*DTP*DCP*DTP*DGP*DGP*DTP*DCP*DCP*DT)-3')
F: DNA (5'-D(*DAP*DGP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DTP*DGP*DGP*DCP*DCP*DTP*DA)-3')


Theoretical massNumber of molelcules
Total (without water)23,9254
Polymers23,9254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-61 kcal/mol
Surface area11330 Å2
MethodPISA
2
C: Transcription factor E2-alpha
D: Neurogenic differentiation factor 1
G: DNA (5'-D(*DTP*DAP*DGP*DGP*DCP*DCP*DAP*DTP*DCP*DTP*DGP*DGP*DTP*DCP*DCP*DT)-3')
H: DNA (5'-D(*DAP*DGP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DTP*DGP*DGP*DCP*DCP*DTP*DA)-3')


Theoretical massNumber of molelcules
Total (without water)23,9254
Polymers23,9254
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-59 kcal/mol
Surface area11630 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-132 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.310, 169.540, 52.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a heterodimer of E47 and NeuroD1 bound to a DNA duplex. There are 2 of these complexes in the asymmetric unit.

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Components

#1: Protein Transcription factor E2-alpha


Mass: 7141.364 Da / Num. of mol.: 2 / Fragment: basic-helix-loop-helix domain
Source method: isolated from a genetically manipulated source
Details: pancreatic beta cells / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tcf3 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P15806*PLUS
#2: Protein Neurogenic differentiation factor 1 / NeuroD1


Mass: 6986.231 Da / Num. of mol.: 2 / Fragment: basic helix-loop-helix domain
Source method: isolated from a genetically manipulated source
Details: pancreatic beta cells / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Neurod1, Neurod / Plasmid: pCDF-1b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q60867
#3: DNA chain DNA (5'-D(*DTP*DAP*DGP*DGP*DCP*DCP*DAP*DTP*DCP*DTP*DGP*DGP*DTP*DCP*DCP*DT)-3')


Mass: 4865.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized oligonucleotide
#4: DNA chain DNA (5'-D(*DAP*DGP*DGP*DAP*DCP*DCP*DAP*DGP*DAP*DTP*DGP*DGP*DCP*DCP*DTP*DA)-3')


Mass: 4932.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized oligonucleotide
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN IN CHAINS A AND C MATCH THE UNP SEQUENCE DATABASE REFERENCE P15806(ISOFORM E47; P15806- ...THE PROTEIN IN CHAINS A AND C MATCH THE UNP SEQUENCE DATABASE REFERENCE P15806(ISOFORM E47; P15806-2), RESIDUES 544-603

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.6
Details: 0.1 mM Imidazole, 0.2 M ammonium citrate dibasic, and 22 % PEG 4000, pH 7.6, EVAPORATION, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Imidazole11
2Imidazole12
3ammonium citrate dibasic12
4PEG 400012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2006
Details: sagittal focusing crystal and vertical focusing double mirror
RadiationMonochromator: SI (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→169.546 Å / Num. obs: 18832 / % possible obs: 97.7 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1 / Num. measured all: 18434 / Num. unique all: 2594 / Rsym value: 0.77 / % possible all: 94.8

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
CNSrefinement
PDB_EXTRACT2data extraction
AUTOMARdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MDY

1mdy


Resolution: 2.5→55.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: optimal B-restraints weight (rweight) in CNS was 0.0198
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1884 9.8 %random
Rwork0.248 ---
all-19270 --
obs-18781 97.5 %-
Solvent computationBsol: 83.749 Å2
Displacement parametersBiso mean: 56.998 Å2
Baniso -1Baniso -2Baniso -3
1--8.549 Å20 Å20 Å2
2---10.084 Å20 Å2
3---18.633 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 1300 0 41 3092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.154
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.4337 197 -
Rwork0.3963 --
obs-1566 94 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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