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- PDB-7jsa: Crystal structure of the DNA binding domain of human transcriptio... -

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Basic information

Entry
Database: PDB / ID: 7jsa
TitleCrystal structure of the DNA binding domain of human transcription factor ERF in the reduced form, in complex with double-stranded DNA ACCGGAAGTG
Components
  • DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
  • DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
  • ETS domain-containing transcription factor ERF
KeywordsDNA BINDING PROTEIN/DNA / Transcription / Tumor suppressor / ETS family / repressor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus ...Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / ETS domain-containing transcription factor ERF
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHou, C. / Tsodikov, O.V.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)PC150300 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA243529 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Insight into the DNA Binding Function of Transcription Factor ERF.
Authors: Hou, C. / McCown, C. / Ivanov, D.N. / Tsodikov, O.V.
History
DepositionAug 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
C: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
J: ETS domain-containing transcription factor ERF


Theoretical massNumber of molelcules
Total (without water)20,3123
Polymers20,3123
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-17 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.798, 63.798, 137.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')


Mass: 3094.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')


Mass: 2995.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others)
#3: Protein ETS domain-containing transcription factor ERF / Ets2 repressor factor / PE-2


Mass: 14222.460 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal region GPHM is an N-terminal tag leftover after cleavage. The C-terminal region starting with KLVL... is disordered.
Source: (gene. exp.) Homo sapiens (human) / Gene: ERF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P50548
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 6% PEG 4000, 0.1M Hepes, 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 7139 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 32
Reflection shellResolution: 2.85→2.9 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 348 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JVT

6jvt


Resolution: 2.85→37.75 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 33.081 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 359 5.1 %RANDOM
Rwork0.2469 ---
obs0.2483 6712 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.88 Å2 / Biso mean: 84.67 Å2 / Biso min: 55.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2---2.03 Å20 Å2
3---4.05 Å2
Refinement stepCycle: final / Resolution: 2.85→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 403 0 1 1163
Biso mean---69.43 -
Num. residues----108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121232
X-RAY DIFFRACTIONr_bond_other_d0.0020.018952
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.461741
X-RAY DIFFRACTIONr_angle_other_deg1.2371.9282209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.472587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88220.81649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2115144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.968157
X-RAY DIFFRACTIONr_chiral_restr0.0530.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
LS refinement shellResolution: 2.853→2.926 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 20 -
Rwork0.39 477 -
all-497 -
obs--96.88 %
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)
10.66290.10141.50893.6619-0.20615.5206-0.36240.39480.1944-0.25460.2846-0.06440.1390.32270.07780.3761-0.1799-0.11120.68940.15260.402-0.057317.969-19.0593
21.77840.5291-0.36223.69920.1062.5898-0.52760.41160.29140.070.1678-0.014-0.18690.08280.35990.2936-0.0398-0.06330.51840.13290.3569-1.696318.8198-18.2721
36.3604-1.0850.82162.0477-0.35653.5429-0.082-0.1262-0.12970.3360.2531-0.3725-0.0408-0.1251-0.17110.390.06670.02940.45930.15870.2136-3.357711.3212-3.6916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 11
2X-RAY DIFFRACTION2C14 - 23
3X-RAY DIFFRACTION3J22 - 109

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