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- PDB-2ypb: Structure of the SCL:E47 complex bound to DNA -

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Basic information

Entry
Database: PDB / ID: 2ypb
TitleStructure of the SCL:E47 complex bound to DNA
Components
  • EBOX FORWARD
  • EBOX REVERSE
  • T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1
  • TRANSCRIPTION FACTOR E2-ALPHA
KeywordsIMMUNE SYSTEM / HEMATOPOIESIS / LEUKEMIA
Function / homology
Function and homology information


hemangioblast cell differentiation / regulation of mast cell differentiation / positive regulation of chromatin organization / astrocyte fate commitment / vitamin D response element binding / basophil differentiation / spinal cord association neuron differentiation / regulation of somatic stem cell population maintenance / megakaryocyte differentiation / bHLH transcription factor binding ...hemangioblast cell differentiation / regulation of mast cell differentiation / positive regulation of chromatin organization / astrocyte fate commitment / vitamin D response element binding / basophil differentiation / spinal cord association neuron differentiation / regulation of somatic stem cell population maintenance / megakaryocyte differentiation / bHLH transcription factor binding / immunoglobulin V(D)J recombination / definitive hemopoiesis / TGFBR3 expression / mitogen-activated protein kinase kinase kinase binding / embryonic hemopoiesis / platelet formation / megakaryocyte development / Myogenesis / erythrocyte maturation / B cell lineage commitment / E-box binding / hemopoiesis / regulation of G1/S transition of mitotic cell cycle / positive regulation of cell division / hematopoietic stem cell differentiation / cell fate commitment / positive regulation of DNA-binding transcription factor activity / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / positive regulation of B cell proliferation / positive regulation of neuron differentiation / positive regulation of mitotic cell cycle / positive regulation of erythrocyte differentiation / B cell differentiation / erythrocyte differentiation / locomotory behavior / positive regulation of protein-containing complex assembly / euchromatin / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / histone deacetylase binding / Transcriptional regulation of granulopoiesis / nervous system development / regulation of cell population proliferation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Helix-loop-helix protein TAL-like / : / 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 / T-cell acute lymphocytic leukemia protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsEl Omari, K. / Hoosdally, S.J. / Tuladhar, K. / Karia, D. / Ponsele, E. / Platonova, O. / Vyas, P. / Patient, R. / Porcher, C. / Mancini, E.J.
CitationJournal: Cell Rep. / Year: 2013
Title: Structural Basis for Lmo2-Driven Recruitment of the Scl:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets.
Authors: El Omari, K. / Hoosdally, S.J. / Tuladhar, K. / Karia, D. / Hall-Ponsele, E. / Platonova, O. / Vyas, P. / Patient, R. / Porcher, C. / Mancini, E.J.
History
DepositionOct 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1
B: TRANSCRIPTION FACTOR E2-ALPHA
E: EBOX FORWARD
F: EBOX REVERSE


Theoretical massNumber of molelcules
Total (without water)27,1024
Polymers27,1024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-54 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.193, 152.882, 55.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1 / TAL-1 / CLASS A BASIC HELIX-LOOP-HELIX PROTEIN 17 / BHLHA17 / STEM CELL PROTEIN / T-CELL ...TAL-1 / CLASS A BASIC HELIX-LOOP-HELIX PROTEIN 17 / BHLHA17 / STEM CELL PROTEIN / T-CELL LEUKEMIA/LYMPHOMA PROTEIN 5 / SCL


Mass: 10721.119 Da / Num. of mol.: 1 / Fragment: BHLH, RESIDUES 5-78
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17542
#2: Protein TRANSCRIPTION FACTOR E2-ALPHA / CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 21 / BHLHB21 / IMMUNOGLOBULIN ENHANCER-BINDING FACTOR ...CLASS B BASIC HELIX-LOOP-HELIX PROTEIN 21 / BHLHB21 / IMMUNOGLOBULIN ENHANCER-BINDING FACTOR E12/E47 / IMMUNOGLOBULIN TRANSCRIPTION FACTOR 1 / KAPPA-E2-BINDING FACTOR / TRANSCRIPTION FACTOR 3 / TCF -3 / TRANSCRIPTION FACTOR ITF-1 / E47


Mass: 9674.212 Da / Num. of mol.: 1 / Fragment: RESIDUES 535-613
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15923
#3: DNA chain EBOX FORWARD


Mass: 3284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#4: DNA chain EBOX REVERSE


Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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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: 2.8 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6
Details: 5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→3 Å / Num. obs: 7203 / % possible obs: 97.8 % / Observed criterion σ(I): 1.2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YPA

2ypa


Resolution: 2.87→42.44 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.937 / SU B: 51.981 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R: 1.563 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.28828 331 4.6 %RANDOM
Rwork0.25381 ---
obs0.25531 6860 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.195 Å2
Baniso -1Baniso -2Baniso -3
1-8.14 Å20 Å20 Å2
2---3.96 Å20 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 2.87→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 448 0 0 1622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0211687
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8042.3062353
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1455139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.27522.87966
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84615249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0821519
X-RAY DIFFRACTIONr_chiral_restr0.0420.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021114
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0571.5703
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.21521131
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2263984
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.8574.51222
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.873→2.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 16 -
Rwork0.4 452 -
obs--86.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.2925-7.53713.734218.326-2.010616.77060.55780.3382-1.1086-0.00520.627-0.0121.11250.6932-1.18480.8610.11990.4390.53-0.12080.6681-8.013-46.27-3.541
212.7289-21.41166.205938.0984-3.796229.71790.7419-0.36020.7458-1.3750.1718-2.0729-0.9591-0.4081-0.91370.1919-0.1924-0.11420.69350.59510.8415-11.977-32.845-4.305
317.9451-24.0896-1.108335.341-5.210515.86-0.0034-0.57870.2992-0.1560.5338-0.13770.0901-0.0115-0.53040.13080.1320.06340.5512-0.14930.371-18.837-20.481-5.19
49.88312.64080.539914.18020.55825.3906-0.06210.14880.8621-0.37810.18150.8544-0.6198-0.0152-0.11940.36560.2536-0.02080.3993-0.1390.4545-24.282-7.044-11.863
540.67826.7188.462549.299111.74363.50910.21860.763-3.03570.15150.2889-0.26090.9838-0.1556-0.50751.8356-0.3891-0.12881.0065-0.12840.7633-34.165-46.618-23.501
612.661920.54462.506849.12029.92532.6794-0.1850.60430.73260.47660.41460.290.2614-0.0472-0.22970.34340.18350.00160.3942-0.07610.3121-25.105-30.316-21.967
77.88454.1286-1.332512.4013-2.38330.715-0.11751.03370.5539-0.93210.073-0.7363-0.15630.17160.04460.7539-0.22940.14970.6625-0.03250.5072-11.061-13.713-16.998
80.7546-4.3699-2.021533.695212.32387.22520.0196-0.02240.37221.5345-0.0919-0.9004-0.593-0.14470.07230.643-0.014-0.08010.4813-0.12920.9281-14.69-2.35-6.72
917.176-8.8029-1.575415.39421.25420.17390.650.59160.0361-1.0431-0.64890.7929-0.1203-0.0634-0.00110.51690.09030.18290.3646-0.07770.2139-23.997-32.852-11.025
1016.427410.3768-0.161618.82462.95490.8074-0.59240.3201-0.07220.42340.37820.56940.28850.19160.21420.35720.21340.25120.60920.11470.2278-6.824-36.294-18.3
1113.587-2.07127.696511.2194-3.088110.16030.4433-0.32640.31570.3092-0.3342-0.10960.72370.3275-0.10920.2484-0.01880.11670.2772-0.03320.1412-8.123-30.592-12.973
124.85383.66893.814210.6468-0.746311.6340.4314-0.5381-0.41680.7409-0.1390.7808-0.6675-0.6092-0.29250.38670.01480.07750.35220.06170.3195-26.325-37.258-13.658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A182 - 192
2X-RAY DIFFRACTION2A193 - 199
3X-RAY DIFFRACTION3A200 - 211
4X-RAY DIFFRACTION4A212 - 247
5X-RAY DIFFRACTION5B539 - 548
6X-RAY DIFFRACTION6B549 - 562
7X-RAY DIFFRACTION7B563 - 586
8X-RAY DIFFRACTION8B587 - 609
9X-RAY DIFFRACTION9E4 - 10
10X-RAY DIFFRACTION10E11 - 14
11X-RAY DIFFRACTION11F22 - 26
12X-RAY DIFFRACTION12F27 - 32

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