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- PDB-3mln: DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (... -

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Basic information

Entry
Database: PDB / ID: 3mln
TitleDNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (crystal form II)
Components
  • DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3')
  • Transcription factor COE1
KeywordsTRANSCRIPTION/DNA / transcription factor / pseudo-Ig-fold / Zn-finger / Zn-knuckle / DNA / TRANSCRIPTION-DNA complex / ebf / ebf-1
Function / homology
Function and homology information


C2H2 zinc finger domain binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding ...C2H2 zinc finger domain binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor COE1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTreiber, N. / Treiber, T. / Zocher, G. / Grosschedl, R.
CitationJournal: Genes Dev. / Year: 2010
Title: Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins
Authors: Treiber, N. / Treiber, T. / Zocher, G. / Grosschedl, R.
History
DepositionApr 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 23, 2015Group: Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.ptnr3_label_seq_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_label_asym_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
E: Transcription factor COE1
C: DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3')
D: DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5917
Polymers90,4605
Non-polymers1312
Water8,017445
1
A: Transcription factor COE1
B: Transcription factor COE1
C: DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3')
D: DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9386
Polymers64,8074
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-24 kcal/mol
Surface area24390 Å2
MethodPISA
2
E: Transcription factor COE1


Theoretical massNumber of molelcules
Total (without water)25,6531
Polymers25,6531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.200, 100.700, 72.000
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcription factor COE1 / Ebf1 / O/E-1 / OE-1 / Early B-cell factor


Mass: 25653.146 Da / Num. of mol.: 3 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ebf1 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q07802
#2: DNA chain DNA (5'-D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)-3')


Mass: 6750.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10% PEG-4000, 200mM KCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 3, 2009
RadiationMonochromator: Bartels / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→29.31 Å / Num. all: 39094 / Num. obs: 38953 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 39 Å2 / Rsym value: 0.083 / Net I/σ(I): 14.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4454 / Rsym value: 0.459 / % possible all: 98

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MLO

3mlo


Resolution: 2.4→29.31 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.38 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21861 1948 5 %RANDOM
Rwork0.17096 ---
obs0.17338 37005 100 %-
all-39094 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.571 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20.31 Å2
2--0.48 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 896 2 445 6007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225837
X-RAY DIFFRACTIONr_angle_refined_deg1.352.1398074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5225599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90623.923260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00815850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3761541
X-RAY DIFFRACTIONr_chiral_restr0.080.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214193
X-RAY DIFFRACTIONr_mcbond_it0.5481.52931
X-RAY DIFFRACTIONr_mcangle_it1.04524741
X-RAY DIFFRACTIONr_scbond_it1.56932906
X-RAY DIFFRACTIONr_scangle_it2.3524.53321
LS refinement shellResolution: 2.395→2.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 131 -
Rwork0.227 2483 -
obs--100 %
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)
11.07240.27660.80861.10560.7543.46780.0093-0.0381-0.0850.06130.0796-0.10640.1567-0.0118-0.0890.09810.0128-0.00150.0306-0.00120.01432.486-10.34933.49
21.53920.37860.00241.99880.80272.2009-0.14890.074-0.2963-0.180.2058-0.23130.23710.0939-0.05690.245-0.02470.06740.0906-0.03390.07412.793-23.104-8.567
32.15870.1770.33953.56331.44616.68210.08190.12110.1146-0.1849-0.04160.2064-0.4359-0.2299-0.04030.07740.0002-0.00540.02710.01260.0215-17.991-36.08212.495
44.92030.5334-0.11171.6213-0.1841.3268-0.18430.22730.2538-0.07970.1696-0.0832-0.07840.01740.01470.06740.0007-0.00940.0939-0.00830.02252.658-4.3958.402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 240
2X-RAY DIFFRACTION2B35 - 247
3X-RAY DIFFRACTION3E27 - 235
4X-RAY DIFFRACTION4C1 - 22
5X-RAY DIFFRACTION4D1 - 22

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