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- PDB-2ypa: Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA -

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Basic information

Entry
Database: PDB / ID: 2ypa
TitleStructure of the SCL:E47:LMO2:LDB1 complex bound to DNA
Components
  • EBOX FORWARD
  • EBOX REVERSE
  • LIM DOMAIN-BINDING PROTEIN 1
  • RHOMBOTIN-2
  • 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 / Expression and translocation of olfactory receptors / spinal cord association neuron differentiation / regulation of kinase activity / cellular component assembly ...hemangioblast cell differentiation / regulation of mast cell differentiation / positive regulation of chromatin organization / astrocyte fate commitment / vitamin D response element binding / basophil differentiation / Expression and translocation of olfactory receptors / spinal cord association neuron differentiation / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / regulation of somatic stem cell population maintenance / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / megakaryocyte differentiation / bHLH transcription factor binding / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / epithelial structure maintenance / LIM domain binding / immunoglobulin V(D)J recombination / gastrulation with mouth forming second / definitive hemopoiesis / TGFBR3 expression / Cardiogenesis / anterior/posterior axis specification / mitogen-activated protein kinase kinase kinase binding / embryonic hemopoiesis / platelet formation / regulation of focal adhesion assembly / megakaryocyte development / Myogenesis / erythrocyte maturation / B cell lineage commitment / cell leading edge / E-box binding / hemopoiesis / regulation of G1/S transition of mitotic cell cycle / positive regulation of cell division / somatic stem cell population maintenance / hair follicle development / 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 cell adhesion / positive regulation of mitotic cell cycle / regulation of cell migration / positive regulation of erythrocyte differentiation / B cell differentiation / erythrocyte differentiation / transcription coregulator binding / transcription coregulator activity / locomotory behavior / positive regulation of protein-containing complex assembly / positive regulation of transcription elongation by RNA polymerase II / euchromatin / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of expression of SLITs and ROBOs / RNA polymerase II transcription regulator complex / histone deacetylase binding / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / neuron differentiation / 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 coactivator activity / transcription cis-regulatory region binding / cell adhesion / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / 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 / metal ion binding / identical protein binding / nucleus
Similarity search - Function
Helix-loop-helix protein TAL-like / : / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B ...Helix-loop-helix protein TAL-like / : / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / 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 / Ribbon / Few Secondary Structures / Irregular / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor E2-alpha / T-cell acute lymphocytic leukemia protein 1 / Rhombotin-2 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: RHOMBOTIN-2
D: LIM DOMAIN-BINDING PROTEIN 1
E: EBOX FORWARD
F: EBOX REVERSE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,61610
Polymers49,3546
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-64 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.966, 141.044, 148.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Protein , 4 types, 4 molecules ABCD

#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 180-253
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 TRANSCRIPT ION 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: Protein RHOMBOTIN-2 / CYSTEINE-RICH PROTEIN TTG-2 / LIM DOMAIN ONLY PROTEIN 2 / LMO-2 / T-CELL TRANSLOCATION PROTEIN 2 / LMO2


Mass: 17007.609 Da / Num. of mol.: 1 / Fragment: LIM, RESIDUES 25-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25791
#4: Protein LIM DOMAIN-BINDING PROTEIN 1 / LDB-1 / CARBOXYL-TERMINAL LIM DOMAIN-BINDING PROTEIN 2 / CLIM-2 / LIM DOMAIN-BINDING FACTOR CLIM2 / ...LDB-1 / CARBOXYL-TERMINAL LIM DOMAIN-BINDING PROTEIN 2 / CLIM-2 / LIM DOMAIN-BINDING FACTOR CLIM2 / HLDB1 / NUCLEAR LIM INTERACTOR / LDB1


Mass: 5244.568 Da / Num. of mol.: 1 / Fragment: LID, RESIDUES 336-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q86U70

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DNA chain , 2 types, 2 molecules EF

#5: DNA chain EBOX FORWARD


Mass: 3284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#6: 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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Non-polymers , 1 types, 4 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 2.7 Å3/Da / Density % sol: 59 % / 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: I04 / Wavelength: 1.2829
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2829 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 16249 / % possible obs: 96.3 % / Observed criterion σ(I): 1.2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.2 / % possible all: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→30.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 39.437 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 1.022 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26945 641 4.8 %RANDOM
Rwork0.22401 ---
obs0.22614 12714 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.707 Å2
Baniso -1Baniso -2Baniso -3
1-6.15 Å20 Å20 Å2
2--1.15 Å20 Å2
3----7.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 448 4 0 2894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0182976
X-RAY DIFFRACTIONr_bond_other_d0.0010.022687
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.8144078
X-RAY DIFFRACTIONr_angle_other_deg0.78936166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.315292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33923.088136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41715492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3461533
X-RAY DIFFRACTIONr_chiral_restr0.0530.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 50 -
Rwork0.408 931 -
obs--98.99 %
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)
13.27650.38020.31160.0457-0.00061.361-0.0328-0.35080.01810.0033-0.03750.0137-0.1858-0.02190.07030.0438-0.02710.06480.2097-0.01990.382235.186415.364913.1801
21.2713-0.19450.13970.18810.38771.09390.1486-0.05940.1251-0.10380.0317-0.0919-0.19020.1255-0.18040.0606-0.01410.07450.20480.03880.414137.318217.36375.8655
30.65050.6937-1.24991.7736-1.97952.89130.0074-0.01840.15620.26550.24530.1172-0.24560.0233-0.25270.1473-0.07760.05420.3599-0.03880.267951.777519.954731.5103
41.65131.1926-2.22161.1227-2.04473.73760.032-0.3883-0.23230.4651-0.5459-0.2824-0.78820.89930.51390.6974-0.4199-0.18550.4720.02270.208360.347226.060233.0081
54.44570.27070.26451.84050.06662.550.4783-0.15310.3089-0.1817-0.440.0344-0.2856-0.7298-0.03830.12310.11440.08610.3069-0.02440.271320.676216.89096.0424
63.0404-2.1698-0.34664.80931.98172.57210.25070.11460.43480.065-0.4463-0.2314-0.0609-0.00860.19560.0795-0.00120.05070.1803-0.02660.316320.569617.71256.6635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A182 - 248
2X-RAY DIFFRACTION2B539 - 612
3X-RAY DIFFRACTION3C30 - 155
4X-RAY DIFFRACTION4D300 - 329
5X-RAY DIFFRACTION5E4 - 14
6X-RAY DIFFRACTION6F22 - 32

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