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

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Basic information

Entry
Database: PDB / ID: 7jsl
TitleCrystal structure of the DNA binding domain of human transcription factor ERF in the oxidized 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: 4.51 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
A: DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
D: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
E: ETS domain-containing transcription factor ERF
F: DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
G: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
H: ETS domain-containing transcription factor ERF
I: DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
K: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
L: ETS domain-containing transcription factor ERF


Theoretical massNumber of molelcules
Total (without water)81,25012
Polymers81,25012
Non-polymers00
Water00
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-19 kcal/mol
Surface area7850 Å2
MethodPISA
2
A: DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
D: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
E: ETS domain-containing transcription factor ERF


Theoretical massNumber of molelcules
Total (without water)20,3123
Polymers20,3123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-19 kcal/mol
Surface area7860 Å2
MethodPISA
3
F: DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
G: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
H: ETS domain-containing transcription factor ERF


Theoretical massNumber of molelcules
Total (without water)20,3123
Polymers20,3123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-19 kcal/mol
Surface area7860 Å2
MethodPISA
4
I: DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
K: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')
L: ETS domain-containing transcription factor ERF


Theoretical massNumber of molelcules
Total (without water)20,3123
Polymers20,3123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-19 kcal/mol
Surface area7890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.537, 128.464, 174.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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.: 4 / 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.: 4 / 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.: 4
Source method: isolated from a genetically manipulated source
Details: The N-terminal region GPHM is a leftover after affinity tag cleavage. The C-terminal region KLVL...SGSS is disordered.
Source: (gene. exp.) Homo sapiens (human) / Gene: ERF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P50548
Has protein modificationY

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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: 4.41 Å3/Da / Density % sol: 72.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 4000, 0.1M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 8678 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.9
Reflection shellResolution: 4.5→4.58 Å / Num. unique obs: 418 / CC1/2: 0.73

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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: 7JSA

7jsa


Resolution: 4.51→36.85 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.946 / SU B: 71.617 / SU ML: 0.784 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.899 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 434 5 %RANDOM
Rwork0.2243 ---
obs0.2263 8243 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 347.29 Å2 / Biso mean: 212.875 Å2 / Biso min: 138.21 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å2-0 Å20 Å2
2--1.2 Å2-0 Å2
3---1.89 Å2
Refinement stepCycle: final / Resolution: 4.51→36.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 1612 0 0 4500
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124778
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183679
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.4536763
X-RAY DIFFRACTIONr_angle_other_deg1.2131.9428533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68820.625192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02515558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5481528
X-RAY DIFFRACTIONr_chiral_restr0.050.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
LS refinement shellResolution: 4.512→4.628 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 19 -
Rwork0.367 563 -
all-582 -
obs--94.17 %

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