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- PDB-3mqi: Human early B-cell factor 1 (EBF1) IPT/TIG domain -

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Basic information

Entry
Database: PDB / ID: 3mqi
TitleHuman early B-cell factor 1 (EBF1) IPT/TIG domain
ComponentsTranscription factor COE1
KeywordsTRANSCRIPTION ACTIVATOR / immunoglobulin like fold / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Expression and translocation of olfactory receptors / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
Transcription factor COE / Transcription factor COE, conserved site / Transcription factor COE, DNA-binding domain / Transcription factor COE, helix-loop-helix domain / Transcription factor COE, IPT domain / Transcription factor COE, DNA-binding domain superfamily / Transcription factor COE1 DNA-binding domain / Transcription factor COE1 helix-loop-helix domain / COE family signature. / IPT/TIG domain ...Transcription factor COE / Transcription factor COE, conserved site / Transcription factor COE, DNA-binding domain / Transcription factor COE, helix-loop-helix domain / Transcription factor COE, IPT domain / Transcription factor COE, DNA-binding domain superfamily / Transcription factor COE1 DNA-binding domain / Transcription factor COE1 helix-loop-helix domain / COE family signature. / IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHYL MERCURY ION / trimethylamine oxide / Transcription factor COE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSiponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. ...Siponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schueler, H. / Schutz, P. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Berglund, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Determination of Functional Domains in Early B-cell Factor (EBF) Family of Transcription Factors Reveals Similarities to Rel DNA-binding Proteins and a Novel Dimerization Motif.
Authors: Siponen, M.I. / Wisniewska, M. / Lehtio, L. / Johansson, I. / Svensson, L. / Raszewski, G. / Nilsson, L. / Sigvardsson, M. / Berglund, H.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: Transcription factor COE1
B: Transcription factor COE1
C: Transcription factor COE1
C: trimethylamine oxide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,90510
Polymers31,4523
Non-polymers1,4537
Water1,36976
1
A: Transcription factor COE1
B: Transcription factor COE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8876
Polymers20,9682
Non-polymers9194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-19 kcal/mol
Surface area9930 Å2
MethodPISA
2
C: Transcription factor COE1
hetero molecules

C: Transcription factor COE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0378
Polymers20,9682
Non-polymers1,0696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1960 Å2
ΔGint-17 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.291, 57.073, 69.140
Angle α, β, γ (deg.)90.00, 93.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription factor COE1 / O/E-1 / OE-1 / Early B-cell factor


Mass: 10484.073 Da / Num. of mol.: 3 / Fragment: IPT/TIG domain (UNP residues 258-351)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COE1, EBF, EBF1, EBF1A / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRARE / References: UniProt: Q9UH73
#2: Chemical
ChemComp-EMC / ETHYL MERCURY ION / Ethylmercury


Mass: 229.651 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 54.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M Tris, 23% PEG MME, 0.3M trimethylamine n-oxide, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.00764 Å
DetectorDetector: CCD / Date: Jun 2, 2009 / Details: mirrors
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00764 Å / Relative weight: 1
ReflectionResolution: 2.3→28.53 Å / Num. obs: 14710 / % possible obs: 13.46 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Biso Wilson estimate: 41.76 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 16.78
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.72 / Num. unique all: 1056 / Rsym value: 0.726 / % possible all: 13.24

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Processing

Software
NameVersionClassification
APEXdata collection
SOLVEphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→28.53 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27275 741 5 %RANDOM
Rwork0.23335 ---
obs0.23532 13970 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20.19 Å2
2---1.77 Å20 Å2
3---0.83 Å2
Refine analyzeLuzzati coordinate error free: 0.253 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 23 76 2154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222129
X-RAY DIFFRACTIONr_bond_other_d00.021426
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9542898
X-RAY DIFFRACTIONr_angle_other_deg4.22733495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20222.77872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78815327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.447159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212299
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02424
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_it0.5591.51336
X-RAY DIFFRACTIONr_mcbond_other01.5541
X-RAY DIFFRACTIONr_mcangle_it1.12922189
X-RAY DIFFRACTIONr_scbond_it1.5413793
X-RAY DIFFRACTIONr_scangle_it2.6734.5709
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 54 -
Rwork0.303 1023 -
obs--96.94 %

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