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- PDB-9db5: A DARPin fused to the 1TEL crystallization chaperone via a prolin... -

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Basic information

Entry
Database: PDB / ID: 9db5
TitleA DARPin fused to the 1TEL crystallization chaperone via a proline-alanine linker
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
ACETIC ACID / Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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
DepositionAug 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6,DARPin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,78023
Polymers25,7801
Non-polymers1,00022
Water2,882160
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)97.730, 97.730, 45.816
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: 25779.832 Da / Num. of mol.: 1
Fragment: residues 47-121 (Uniprot numbering) of Transcription factor ETV6
Source method: isolated from a genetically manipulated source
Details: Pro-Ala linking the ETV6 and the DARPin
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ETV6, TEL, TEL1 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41212
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.46 Å3/Da / Density % sol: 49.96 % / Description: Thin rod
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.6
Details: 4.0 M Ammonium acetate, 0.1 M Sodium acetate trihydrate

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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: Jun 14, 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: 1.57→48.87 Å / Num. obs: 33052 / % possible obs: 94.1 % / Redundancy: 13.7 % / Biso Wilson estimate: 17.08 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2162 / Rpim(I) all: 0.05997 / Rrim(I) all: 0.2246 / Net I/σ(I): 12.34
Reflection shellResolution: 1.57→1.626 Å / Redundancy: 14.3 % / Rmerge(I) obs: 4.199 / Mean I/σ(I) obs: 1.38 / Num. unique obs: 3468 / CC1/2: 0.501 / CC star: 0.817 / Rpim(I) all: 1.14 / Rrim(I) all: 4.353 / % possible all: 99.54

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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: 1.57→48.87 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1963 1585 -
Rwork0.1671 31592 -
obs-33052 94.1 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 61 160 2007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091869
X-RAY DIFFRACTIONf_angle_d1.05182532
X-RAY DIFFRACTIONf_chiral_restr0.0586284
X-RAY DIFFRACTIONf_plane_restr0.008342
X-RAY DIFFRACTIONf_dihedral_angle_d5.2098248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.620.27251720.25542985X-RAY DIFFRACTION99.62
1.62-1.680.24041250.22933061X-RAY DIFFRACTION99.94
1.68-1.740.2651140.22492627X-RAY DIFFRACTION85.98
1.74-1.820.26851540.19163032X-RAY DIFFRACTION100
1.82-1.920.23611280.19762547X-RAY DIFFRACTION83.67
1.92-2.040.1911490.17122812X-RAY DIFFRACTION92.71
2.04-2.20.17431570.14482722X-RAY DIFFRACTION90.19
2.2-2.420.17481290.14852902X-RAY DIFFRACTION94.69
2.42-2.770.15241570.15082866X-RAY DIFFRACTION94.03
2.77-3.480.18681560.15962999X-RAY DIFFRACTION97.77
3.49-48.870.20031630.15813039X-RAY DIFFRACTION96.94
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)
13.29075034385-1.753625255380.7924173171335.81347107816-2.355432326171.004906505940.009401990028130.3760681390980.384472285415-0.325296862846-0.040056351012-0.591769344708-0.727420961930.5179598537160.03490750857530.267475524322-0.06221170764990.02715045940830.1632413498790.001294886896870.20100957392530.41646519634.9118074492936.1806344453
21.669655409440.09675949177750.4990646579344.913591592980.1434348907260.8773918791530.024440800292-0.136449733125-0.01227462514590.180412560723-0.01658895279630.113901752069-0.0235008396467-0.0980759132813-0.008962417371980.1068154876680.004639819062760.01210956451630.1122118829390.003583960841290.05950039773718.75485049845.4935118926442.4968906908
30.344095553843-1.83957623649-1.77660214743.874519279353.33395137782.20450557191-0.0007683431174470.003908311770730.0359872327465-0.2133495819880.002363880460790.013714007792-0.2105808146550.0298740809406-0.01200145869160.105980637372-0.00138479993035-0.01390203915050.142117729142-0.01965839329590.11807603147923.0407406848-6.9510512713325.8692162009
42.62974420304-0.955822556701-0.2885497890863.549622153460.9576287198474.223690278230.0174811624086-0.0704869151195-0.1664035712170.0452326285539-0.0006589907895910.06622356326770.218166657315-0.0807100760086-0.005240196256870.08991188894220.00469949357116-0.009573936352030.079461435841-0.002694546977910.11670387969126.0309321432-26.690040868119.724510034
54.77137830705-1.01842667546-1.26653411354.62661535342.353590997614.987999407050.1315041899110.0923135754406-0.139016295337-0.0959974173634-0.0112680210763-0.03144018330440.3547125565930.0947231826541-0.1173020373170.2441138448120.0672656597778-0.02088096431770.0934351833066-0.02856976791430.18059515983631.9934788548-38.318003762913.8120533371
64.36873348176-0.270720972668-1.392050164271.78410935592-1.637858872557.2929700195-0.106229920321-0.261131930834-0.06214795116150.341726272925-0.0517440151835-0.0493019802939-0.2675371010590.2291312967850.1811018293980.3117903887980.08333133044680.0287482007070.1561785285150.01715804058510.2658135872638.9417044853-44.684620715313.8253817575
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 2 through 17 )2 - 171 - 16
22chain 'A' and (resid 18 through 64 )18 - 6417 - 63
33chain 'A' and (resid 65 through 115 )65 - 11564 - 114
44chain 'A' and (resid 116 through 181 )116 - 181115 - 180
55chain 'A' and (resid 182 through 214 )182 - 214181 - 213
66chain 'A' and (resid 215 through 235 )215 - 235214 - 234

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