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- PDB-9dam: Crystal Structure of a DARPin Fused to the 1TEL Crystallization C... -

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Basic information

Entry
Database: PDB / ID: 9dam
TitleCrystal Structure of a DARPin Fused to the 1TEL Crystallization Chaperone via a Direct Helical Fusion in a 3-Fold Crystal Form
ComponentsTranscription factor ETV6 fused to a 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
ACETIC ACID / Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsPedroza Romo, M.J. / Averett, J.C. / Keliiliki, A. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E.W. / Nickles, R. ...Pedroza Romo, M.J. / Averett, J.C. / Keliiliki, A. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E.W. / Nickles, R. / 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.W. / Nickles, R. / Doukov, T. / Moody, J.D.
History
DepositionAug 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor ETV6 fused to a DARPin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3178
Polymers27,0791
Non-polymers2387
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.290, 83.290, 58.434
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcription factor ETV6 fused to a DARPin


Mass: 27079.338 Da / Num. of mol.: 1
Fragment: residues 47-121 (Uniprot numbering) of the ETV6 portion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ETV6, TEL, TEL1 / Plasmid: pET42_SUMO / Details (production host): kanamycin resistant / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): B / References: UniProt: P41212

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Non-polymers , 5 types, 131 molecules

#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 42 %
Description: Hexagonal prism, tapered to a point, round edges
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.6
Details: 1.0 M Magnesium sulfate hydrate, 0.1 M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 6, 2024
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.78→45.4 Å / Num. obs: 22160 / % possible obs: 97.23 % / Redundancy: 21 % / Biso Wilson estimate: 30.93 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1516 / Rpim(I) all: 0.03361 / Rrim(I) all: 0.1553 / Net I/σ(I): 14.13
Reflection shellResolution: 1.78→1.844 Å / Redundancy: 20.2 % / Rmerge(I) obs: 5.909 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1639 / CC1/2: 0.335 / CC star: 0.708 / Rpim(I) all: 1.332 / Rrim(I) all: 6.06 / % possible all: 75.01

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→45.4 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 1061 4.89 %
Rwork0.2045 20631 -
obs0.2053 21692 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 1.78→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 10 124 1909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01191831
X-RAY DIFFRACTIONf_angle_d1.02032500
X-RAY DIFFRACTIONf_chiral_restr0.0582285
X-RAY DIFFRACTIONf_plane_restr0.0054331
X-RAY DIFFRACTIONf_dihedral_angle_d13.0391625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.860.37011050.32832038X-RAY DIFFRACTION76.95
1.86-1.950.31411280.29422645X-RAY DIFFRACTION99.86
1.95-2.080.24241280.24962663X-RAY DIFFRACTION100
2.08-2.240.22651340.22632635X-RAY DIFFRACTION99.89
2.24-2.460.25221560.21352632X-RAY DIFFRACTION100
2.46-2.820.2241470.20482640X-RAY DIFFRACTION99.01
2.82-3.550.21291250.19662663X-RAY DIFFRACTION99.96
3.55-45.40.19191380.17992715X-RAY DIFFRACTION99.3

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