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- PDB-9e4q: A DARPin fused to the 3TEL crystallization chaperone via a gly-gl... -

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Basic information

Entry
Database: PDB / ID: 9e4q
TitleA DARPin fused to the 3TEL crystallization chaperone via a gly-gly-gly fusion
ComponentsTranscription factor ETV6,DARPin
KeywordsPROTEIN BINDING / TELSAM / DARPin / ETV6 / Designed Ankyrin Repeat Protein
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / neurogenesis / Signaling by FLT3 fusion proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsPedroza Romo, M.J. / Noakes, E. / Soleimani, S. / Smith, T. / Doukov, T. / Moody, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM146209 United States
CitationJournal: To Be Published
Title: Optimal TELSAM-Target Protein Linker Character is Target Protein Dependent
Authors: Pedroza Romo, M.J. / Averett, J.C. / Keliiliki, A. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E. / Nickles, R. / Soleimani, S. / Doukov, T. / Moody, J.D.
History
DepositionOct 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor ETV6,DARPin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8914
Polymers45,6031
Non-polymers2883
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.140, 85.500, 120.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Transcription factor ETV6,DARPin / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 45603.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ETV6, TEL, TEL1 / Production host: Escherichia coli B (bacteria) / Strain (production host): B / Variant (production host): BL21(DE3) / References: UniProt: P41212
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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 Å3/Da / Density % sol: 38.52 % / Description: Needles with a hexagonal cross section
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5, Polyethylene glycol 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2021
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.58→42.75 Å / Num. obs: 6014 / % possible obs: 99.59 % / Redundancy: 12.6 % / Biso Wilson estimate: 80 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.2825 / Rpim(I) all: 0.08171 / Rrim(I) all: 0.2945 / Net I/σ(I): 8.55
Reflection shellResolution: 3.58→3.708 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.132 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 586 / CC1/2: 0.828 / CC star: 0.952 / Rpim(I) all: 0.3483 / Rrim(I) all: 1.187 / % possible all: 98.99

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.58→42.75 Å / SU ML: 0.4587 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3244 310 5.15 %
Rwork0.2684 5704 -
obs0.2711 6014 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.68 Å2
Refinement stepCycle: LAST / Resolution: 3.58→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 15 12 2612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332667
X-RAY DIFFRACTIONf_angle_d0.50383671
X-RAY DIFFRACTIONf_chiral_restr0.0382421
X-RAY DIFFRACTIONf_plane_restr0.0042488
X-RAY DIFFRACTIONf_dihedral_angle_d9.1621838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-4.510.32781740.27242768X-RAY DIFFRACTION99.76
4.51-42.750.32141360.26582936X-RAY DIFFRACTION99.55
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)
12.70099129769-0.726966112718-2.571646798892.396026707292.156871407736.380421540930.415216165568-0.02404134268340.455727819096-0.331919013305-0.06928164440810.182394325233-1.307829138790.062182110665-0.4889882862110.492208274935-0.07372038793280.03095858088320.3477137699080.09979384954360.73945552967615.849787946740.9735747868-1.22883278851
21.30298304699-0.477494309633-0.908117839836.05528675295-0.05018629412112.702300831820.148063922240.1614531710470.2340825270460.196960198541-0.00540064980557-0.365959147272-0.1026738452280.0162637022249-0.1336942841530.31018121460.005768915413650.003910808973880.47022566461-0.0373054957620.39374284618826.15939215723.185417572-17.9548641589
31.973597015133.204094079780.3908089042914.747522103720.2531621093956.420478285230.342379500108-0.4904622203680.2147203398591.08936926096-0.22191400730.27693710698-0.269746895377-0.162469985634-0.1600173324470.492703429503-0.008287575319620.1068101503170.533960253232-0.01647497050780.5849764355311.2888060372-8.76748447105-19.0027002886
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 12 through 102 )12 - 1021 - 82
22chain 'A' and (resid 103 through 261 )103 - 26183 - 228
33chain 'A' and (resid 262 through 402 )262 - 402229 - 369

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