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- PDB-3mlp: Early B-cell Factor 1 (Ebf1) bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3mlp
TitleEarly B-cell Factor 1 (Ebf1) bound to DNA
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 / TIG-domain / IPT-domain / helix-loop-helix / DNA / zinc-finger / zinc-knuckle / 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 / 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
CITRIC ACID / DNA / DNA (> 10) / Transcription factor COE1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Feb 12, 2014Group: Refinement description
Revision 1.3Dec 23, 2015Group: Structure summary
Revision 1.4Nov 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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
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')
E: Transcription factor COE1
F: Transcription factor COE1
G: 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')
H: 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)210,22317
Polymers209,0018
Non-polymers1,2229
Water2,702150
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)105,2089
Polymers104,5014
Non-polymers7075
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-48 kcal/mol
Surface area39590 Å2
MethodPISA
2
E: Transcription factor COE1
F: Transcription factor COE1
G: 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')
H: 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)105,0168
Polymers104,5014
Non-polymers5154
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-32 kcal/mol
Surface area35180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.490, 78.690, 103.570
Angle α, β, γ (deg.)88.99, 90.00, 77.81
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 45499.914 Da / Num. of mol.: 4 / Fragment: DNA binding domain / Mutation: aa 252-258 deleted, H259A
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 10% PEG4000, 10% isopropanol, 100mM sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9537 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 53552 / Num. obs: 52163 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 49.2 Å2 / Rsym value: 0.089 / Net I/σ(I): 9.9
Reflection shellResolution: 2.8→3 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.46 / % possible all: 96.2

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Processing

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

3mln


Resolution: 2.8→38.75 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.876 / SU B: 37.677 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 1.695 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26411 2592 5 %RANDOM
Rwork0.20355 ---
obs0.20661 49243 100 %-
all-52163 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.366 Å2
Baniso -1Baniso -2Baniso -3
1-4.02 Å2-1.21 Å2-0.63 Å2
2---0.05 Å20.95 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9950 1792 69 150 11961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212230
X-RAY DIFFRACTIONr_bond_other_d0.0010.027797
X-RAY DIFFRACTIONr_angle_refined_deg1.4112.14116926
X-RAY DIFFRACTIONr_angle_other_deg0.858319028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17651261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35223.685483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.449151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2931578
X-RAY DIFFRACTIONr_chiral_restr0.0710.21869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022292
X-RAY DIFFRACTIONr_mcbond_it0.87646322
X-RAY DIFFRACTIONr_mcbond_other0.24142555
X-RAY DIFFRACTIONr_mcangle_it1.464410223
X-RAY DIFFRACTIONr_scbond_it1.63665908
X-RAY DIFFRACTIONr_scangle_it2.32666703
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 190 -
Rwork0.311 3616 -
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)
12.2483-0.30760.1172.6378-0.70294.0862-0.1231-0.1322-0.12670.1434-0.0205-0.35330.36420.33150.14360.3615-0.0006-0.0090.1916-0.01950.2862.034-28.0285-4.0421
22.5637-0.29240.63722.93160.62384.14750.01920.0648-0.2122-0.3801-0.0238-0.33490.36710.24690.00460.54070.01660.10970.33260.01560.25282.5803-32.398-47.4588
31.7408-0.167-0.13181.7040.00291.9097-0.21190.12610.3244-0.08260.1375-0.2728-0.02810.10190.07440.2658-0.02520.01570.3062-0.01360.26432.3096-16.9663-27.0729
42.76720.4707-1.31291.8063-1.04754.6035-0.09480.0630.0773-0.17390.0817-0.0579-0.3603-0.0140.01320.3302-0.0011-0.04540.1639-0.01990.27972.429316.3033-31.1244
52.50870.7079-0.4292.31970.09193.65390.1543-0.08190.11030.2814-0.0629-0.0964-0.39490.0524-0.09140.3454-0.028-0.00460.17820.05560.2522.840820.784312.1986
62.5184-0.1253-0.58231.481-0.05091.9999-0.12950.2059-0.4699-0.01850.1307-0.17480.05150.0646-0.00120.23960.0396-0.0560.19640.00810.26952.57195.4289-7.971
75.03941.05850.54826.165-1.47218.22030.0432-0.12140.2188-0.31950.10190.85020.0199-1.4819-0.14510.5486-0.06770.00990.6704-0.00030.4667-22.25087.6983-46.2696
86.66480.92021.71663.0981.056912.63270.16240.1452-0.01380.0510.0645-0.24610.14520.5199-0.22690.4474-0.05940.01960.23930.03360.2569-7.00655.4326-64.9834
94.7050.7624-1.92835.6831-1.72649.11480.1380.0595-0.1580.80220.0170.9942-0.3463-1.3925-0.15490.70350.03490.02670.6001-0.04450.488-22.8447-19.869510.7655
105.3588-1.7326-2.96785.17871.819711.34890.2865-0.6320.2653-0.01650.0917-0.3582-0.01820.9229-0.37810.7404-0.0115-0.11380.3231-0.01470.3324-7.4415-16.849429.9863
112.0425-3.37862.10146.1537-3.66022.2851-0.3174-0.6751-0.34721.08530.54090.2164-0.759-0.6522-0.22361.25110.2086-0.16491.56750.17661.1769-31.949822.2082-77.6078
120.46261.8928-0.23528.6667-0.43970.4301-0.06620.3480.364-0.33830.52091.0514-0.2305-0.6914-0.45471.27080.3150.05651.38550.17751.39-25.980120.5511-74.8061
130.0980.1506-0.00680.29150.11830.49030.04120.04030.01440.0459-0.0108-0.0604-0.0249-0.0304-0.03040.28050.0971-0.02360.39250.01750.3624-1.24-2.212-18.829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 242
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B36 - 242
4X-RAY DIFFRACTION2B501
5X-RAY DIFFRACTION3C1 - 22
6X-RAY DIFFRACTION3D1 - 22
7X-RAY DIFFRACTION4E36 - 242
8X-RAY DIFFRACTION4E501
9X-RAY DIFFRACTION5F36 - 241
10X-RAY DIFFRACTION5F501
11X-RAY DIFFRACTION6G1 - 22
12X-RAY DIFFRACTION6H1 - 22
13X-RAY DIFFRACTION7A243 - 338
14X-RAY DIFFRACTION8B252 - 338
15X-RAY DIFFRACTION9E243 - 338
16X-RAY DIFFRACTION10F250 - 341
17X-RAY DIFFRACTION11A342 - 355
18X-RAY DIFFRACTION11A367 - 386
19X-RAY DIFFRACTION12B339 - 357
20X-RAY DIFFRACTION12B365 - 383
21X-RAY DIFFRACTION13A2 - 15
22X-RAY DIFFRACTION13A426 - 456
23X-RAY DIFFRACTION13B1 - 22
24X-RAY DIFFRACTION13B426 - 443
25X-RAY DIFFRACTION13C23 - 88
26X-RAY DIFFRACTION13D23 - 152
27X-RAY DIFFRACTION13E14 - 23
28X-RAY DIFFRACTION13E426 - 455
29X-RAY DIFFRACTION13F10 - 17
30X-RAY DIFFRACTION13F426 - 457
31X-RAY DIFFRACTION13G23 - 153
32X-RAY DIFFRACTION13H23 - 145

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