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- PDB-4avp: Crystal structure of the DNA-binding domain of human ETV1. -

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Basic information

Entry
Database: PDB / ID: 4avp
TitleCrystal structure of the DNA-binding domain of human ETV1.
ComponentsETS TRANSLOCATION VARIANT 1
KeywordsTRANSCRIPTION / TRANSCRIPTIONAL ACTIVATION AND REPRESSION / DNA BINDING PROTEIN / E TWENTY-SIX / ERWING SARCOMA / PROSTATE CANCER / MELANOMA / GASTROINTESTINAL STROMAL TUMOUR
Function / homology
Function and homology information


peripheral nervous system neuron development / mechanosensory behavior / muscle organ development / axon guidance / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...peripheral nervous system neuron development / mechanosensory behavior / muscle organ development / axon guidance / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
PEA3-type ETS-domain transcription factor, N-terminal / PEA3 subfamily ETS-domain transcription factor N terminal domain / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...PEA3-type ETS-domain transcription factor, N-terminal / PEA3 subfamily ETS-domain transcription factor N terminal domain / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETS translocation variant 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsAllerston, C.K. / Cooper, C.D.O. / Krojer, T. / Chaikuad, A. / Filippakopoulos, P. / Canning, P. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Gileadi, O.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structures of the Ets Domains of Transcription Factors Etv1, Etv4, Etv5 and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation.
Authors: Cooper, C.D.O. / Newman, J.A. / Aitkenhead, H. / Allerston, C.K. / Gileadi, O.
History
DepositionMay 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 25, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs ..._pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.5Dec 20, 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 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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: ETS TRANSLOCATION VARIANT 1
B: ETS TRANSLOCATION VARIANT 1
C: ETS TRANSLOCATION VARIANT 1
D: ETS TRANSLOCATION VARIANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8736
Polymers49,7494
Non-polymers1242
Water3,477193
1
A: ETS TRANSLOCATION VARIANT 1
B: ETS TRANSLOCATION VARIANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9363
Polymers24,8742
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-24 kcal/mol
Surface area9640 Å2
MethodPISA
2
C: ETS TRANSLOCATION VARIANT 1
D: ETS TRANSLOCATION VARIANT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9363
Polymers24,8742
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-22.3 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.317, 45.607, 55.406
Angle α, β, γ (deg.)77.89, 84.80, 90.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given)

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Components

#1: Protein
ETS TRANSLOCATION VARIANT 1 / ETS-RELATED PROTEIN 81


Mass: 12437.209 Da / Num. of mol.: 4 / Fragment: DNA-BINDING DOMAIN, RESIDUES 326-429 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P50549
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 329 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 329 TO SER ...ENGINEERED RESIDUE IN CHAIN A, TYR 329 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 329 TO SER ENGINEERED RESIDUE IN CHAIN C, TYR 329 TO SER ENGINEERED RESIDUE IN CHAIN D, TYR 329 TO SER

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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: 1.72 Å3/Da / Density % sol: 28.55 % / Description: NONE
Crystal growpH: 7.5 / Details: 2.5M SODIUM FORMATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: MARRESEARCH MARMOSAIC 300 / Detector: CCD / Date: Apr 29, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.82→53.94 Å / Num. obs: 27819 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 22.04 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / Rpim(I) all: 0.36 / % possible all: 96.2

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
autoPROCdata reduction
AP_SCALEdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GVJ

1gvj


Resolution: 1.82→53.94 Å / Cor.coef. Fo:Fc: 0.9259 / Cor.coef. Fo:Fc free: 0.8979 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.161
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1401 5.06 %RANDOM
Rwork0.2207 ---
obs0.2227 27704 97.36 %-
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.085 Å20.4741 Å2-1.6649 Å2
2--2.7315 Å20.4987 Å2
3---2.3535 Å2
Refinement stepCycle: LAST / Resolution: 1.82→53.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 8 193 3205
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013149HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.934263HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1437SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes463HARMONIC5
X-RAY DIFFRACTIONt_it3149HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion2.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion380SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4006SEMIHARMONIC4
LS refinement shellResolution: 1.82→1.89 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3192 123 4.31 %
Rwork0.2335 2734 -
all0.2371 2857 -
obs--97.36 %

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