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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 / DNA-binding transcription factor activity, RNA polymerase II-specific ...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 / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / 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: 3.542 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: Biorxiv / Year: 2025
Title: Optimal TELSAM-Target Protein Linker Character is Target Protein-Dependent.
Authors: Romo, M.J.P. / Keliiliki, A. / Averett, J.C. / Gonzalez, J.F. / Noakes, E. / Wilson, E.W. / Smith, C. / Averett, B. / Hansen, D. / Nickles, R. / Bradford, M. / Soleimani, S. / Smith, T. / ...Authors: Romo, M.J.P. / Keliiliki, A. / Averett, J.C. / Gonzalez, J.F. / Noakes, E. / Wilson, E.W. / Smith, C. / Averett, B. / Hansen, D. / Nickles, R. / Bradford, M. / Soleimani, S. / Smith, T. / Nawarathnage, S. / Samarwickrama, P. / Kelsch, A. / Bunn, D. / Stewart, C. / Abiodun, W. / Tsubaki, E. / Brown, S. / Doukov, T.I. / 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
Revision 2.0Dec 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_ref_seq_dif
Item: _entity.formula_weight / _entity.pdbx_mutation ..._entity.formula_weight / _entity.pdbx_mutation / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _software.classification / _software.name / _software.version / _struct_ref_seq_dif.details
Description: Sequence discrepancy
Details: The sequence was wrong at positions 90 and 91. The changes were R90K and D91K. We would like to request that mutations V112E in ETV6 be included in the structure description as well.
Provider: author / Type: Coordinate replacement
Revision 2.1Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)27,0931
Polymers27,0931
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 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 27093.258 Da / Num. of mol.: 1 / Mutation: V112E in ETV6 (Uniprot numbering)
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: 3.542→43.93 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: 3.542→3.668 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
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.542→43.93 Å / SU ML: 0.239 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1123
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.301 158 4.44 %
Rwork0.2644 3402 -
obs0.2679 3559 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195.12 Å2
Refinement stepCycle: LAST / Resolution: 3.542→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 0 0 1722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00371767
X-RAY DIFFRACTIONf_angle_d0.65682410
X-RAY DIFFRACTIONf_chiral_restr0.0406276
X-RAY DIFFRACTIONf_plane_restr0.0064319
X-RAY DIFFRACTIONf_dihedral_angle_d12.575619
LS refinement shellResolution: 3.542→43.93 Å
RfactorNum. reflection% reflection
Rfree0.301 158 -
Rwork0.2644 3559 -
obs--99.97 %
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)
12.20565403690.0745552546230.5876267222732.151170594350.6317616852945.3888495557-0.362269849706-0.8712946568880.6855078154110.3430904051340.7496612074710.116316847427-1.60836557099-1.84426537727-0.354549881140.8598039328340.418752303120.08594067734830.9957161486550.02875867937730.737661020727-15.707313095715.49633970945.23071979375
22.66362206301-1.786443701822.004639004834.77148244318-3.524225027874.094005904250.3588534305660.7047151243791.25487290307-1.656669697240.5832716712481.81705052288-0.017151446527-0.847371189351-0.7870121297732.368619814630.3142584889040.03272964417071.431862816470.5481392440751.98544971414-27.474609146531.0517809949-18.8718426139
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 13 through 75 )13 - 751 - 63
22chain 'A' and (resid 76 through 240 )76 - 24064 - 228

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