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

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Basic information

Entry
Database: PDB / ID: 9dvg
TitleCrystal Structure of a DARPin Fused to the 1TEL Crystallization Chaperone via a Direct Helical Fusion in a 2-Fold Crystal Form
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: 3.54 Å
AuthorsPedroza Romo, M.J. / Averett, J.C. / Keliiliki, A. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E. / Nickles, R. ...Pedroza Romo, M.J. / Averett, J.C. / Keliiliki, A. / Wilson, E.W. / Smith, C. / Hansen, D. / Averett, B. / Gonzalez, J. / Noakes, E. / 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. / Nickles, R. / Doukov, T. / Moody, J.D.
History
DepositionOct 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 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,DARPin


Theoretical massNumber of molelcules
Total (without water)27,0791
Polymers27,0791
Non-polymers00
Water00
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)101.461, 101.461, 48.077
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

#1: Protein Transcription factor ETV6,DARPin


Mass: 27079.338 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
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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5 M Ammonium Phosphate Dibasic, 0.1 M Tris

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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 EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2023
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.54→50.73 Å / Num. obs: 3560 / % possible obs: 99.92 % / Redundancy: 20.6 % / Biso Wilson estimate: 135.55 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1917 / Rpim(I) all: 0.04311 / Rrim(I) all: 0.1966 / Net I/σ(I): 8.12
Reflection shellResolution: 3.54→3.67 Å / Redundancy: 17.3 % / Rmerge(I) obs: 2.487 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 359 / CC1/2: 0.407 / CC star: 0.761 / Rpim(I) all: 0.6086 / Rrim(I) all: 2.562 / % possible all: 100

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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: 3.54→50.73 Å / SU ML: 0.6795 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.0093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3026 163 4.58 %
Rwork0.2953 3397 -
obs0.2954 3560 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 156.62 Å2
Refinement stepCycle: LAST / Resolution: 3.54→50.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 0 0 1721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371787
X-RAY DIFFRACTIONf_angle_d0.66552439
X-RAY DIFFRACTIONf_chiral_restr0.0405279
X-RAY DIFFRACTIONf_plane_restr0.0059322
X-RAY DIFFRACTIONf_dihedral_angle_d12.0389634
LS refinement shellResolution: 3.54→50.73 Å
RfactorNum. reflection% reflection
Rfree0.3026 163 -
Rwork0.2953 3397 -
obs--99.97 %

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