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- PDB-7n2b: A DARPin semi-rigidly fused to the 3TEL crystallization chaperone -

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Basic information

Entry
Database: PDB / ID: 7n2b
TitleA DARPin semi-rigidly fused to the 3TEL crystallization chaperone
ComponentsTranscription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin
KeywordsPROTEIN BINDING / Designed Ankyrin repeat protein / Translocation ETS Leukemia / Sterile Alpha Motif / polymer
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. / Transcription Factor, Ets-1 / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor ETV6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.221 Å
AuthorsSarath Nawarathange, S.D. / Gajjar, P. / Bunn, D. / Stewart, C. / Doukov, T. / Moody, J.D.
CitationJournal: Open Biology / Year: 2022
Title: Crystals of TELSAM-target protein fusions that exhibit minimal crystal contacts and lack direct inter-TELSAM contacts.
Authors: Nawarathnage, S. / Soleimani, S. / Mathis, M.H. / Bezzant, B.D. / Ramirez, D.T. / Gajjar, P. / Bunn, D.R. / Stewart, C. / Smith, T. / Pedroza Romo, M.J. / Brown, S. / Doukov, T. / Moody, J.D.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin
B: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin


Theoretical massNumber of molelcules
Total (without water)93,6352
Polymers93,6352
Non-polymers00
Water00
1
A: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin


Theoretical massNumber of molelcules
Total (without water)46,8181
Polymers46,8181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin


Theoretical massNumber of molelcules
Total (without water)46,8181
Polymers46,8181
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.962, 63.625, 166.005
Angle α, β, γ (deg.)90.000, 90.162, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Transcription factor ETV6,Transcription factor ETV6,Transcription factor ETV6,3TEL-rigid-DARPin / ETS translocation variant 6 / ETS-related protein Tel1 / Tel


Mass: 46817.559 Da / Num. of mol.: 2 / Mutation: V67E
Source method: isolated from a genetically manipulated source
Details: the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the ...Details: the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered,the 3TEL domain forms a helical polymer as the pH is lowered
Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212

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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: 2.6 Å3/Da / Density % sol: 52.61 % / Description: Thin circular or half-moon plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 200 mM L-Proline, 100 mM HEPES, 10 % w/v Polyethylene glycol 3350

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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: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.221→40.16 Å / Num. obs: 13842 / % possible obs: 87.26 % / Redundancy: 3.3 % / Biso Wilson estimate: 84.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07087 / Rrim(I) all: 0.08449 / Net I/σ(I): 10.98
Reflection shellResolution: 3.221→3.336 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5057 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 1491 / CC1/2: 0.906 / CC star: 0.975 / Rpim(I) all: 0.3275 / Rrim(I) all: 0.6052 / % possible all: 95.36

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Processing

Software
NameVersionClassification
Coot0.9model building
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QAR, 4J7W

2qar

4j7w


Resolution: 3.221→40.16 Å / SU ML: 0.4014 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The dataset was initially scaled into space group P212121 and phased with 1 molecule in the AU, but scaling into space group P1211 and phasing with 2 molecules in the AU gave superior refinement statistics.
RfactorNum. reflection% reflection
Rfree0.2425 681 4.94 %
Rwork0.2264 13096 -
obs0.2273 13777 87.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.51 Å2
Refinement stepCycle: LAST / Resolution: 3.221→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 0 0 6067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336206
X-RAY DIFFRACTIONf_angle_d0.56258483
X-RAY DIFFRACTIONf_chiral_restr0.0393968
X-RAY DIFFRACTIONf_plane_restr0.00541113
X-RAY DIFFRACTIONf_dihedral_angle_d11.14072121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.22-3.470.37591090.31662252X-RAY DIFFRACTION75.97
3.47-3.820.33951230.27492510X-RAY DIFFRACTION83.8
3.82-4.370.24381340.22372493X-RAY DIFFRACTION84.01
4.37-5.50.24081510.22992860X-RAY DIFFRACTION95.74
5.51-41.750.19131640.19372981X-RAY DIFFRACTION96.74
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)
12.343110453510.8747071844482.353412656843.685569858781.126259039845.586139399480.394434583743-0.270691619816-0.1129852870080.545903512559-0.315510108311-0.01432345372670.592126477484-0.281179680064-0.0566553205020.718893871115-0.04096230743410.1086167165340.4300467147360.0145081254540.601491645224-4.44310941214-6.0537924262850.7038023555
24.63416247747-2.20469977267-3.992071401920.4501470619141.641584712941.348258041740.2147120830060.108109657594-0.356566551174-0.140888834444-0.562438226999-0.0393419058333-0.5137921393450.2978709528190.2813630653741.067757288990.0683085266355-0.06381920523450.832247622344-0.03260767620550.7521899112018.82543759353-17.062002471516.5033754056
38.26542474682-4.58505616156-2.070582464348.456926754591.939089311053.41449007877-0.471169086585-0.01008594970970.1461967249960.488763993720.334219998982-1.262814193810.2948478286140.2613483883550.134757092840.98712417674-0.02553416141280.002292989802250.5071836977420.07595599225670.69385663322436.4366811554-30.44185433766.01960821407
43.20600649914-1.63710827058-4.280803260463.993656746842.583400274189.288030724480.290374234430.2138622673670.0666526469764-0.225801638489-0.3078617163320.167972392642-0.453451687104-0.237953105791-0.02124736268750.551942870877-0.0106815741115-0.1502223541390.3891571494460.02621720937050.499555363358-27.401654364418.746589952932.3174531534
55.644229372572.392090973544.425968377870.4020022262541.430055592563.196976159940.393070795934-0.4904197252270.2828790229580.229207792551-0.613100681254-0.05044343618360.478387564914-0.163713437494-0.1517994432691.08495801129-0.08980458976060.02842225298860.736959848435-0.02641914017960.810299776159-14.021846700229.812382650266.8526969711
68.001502241063.116185310582.493910416096.384950020470.5705754712063.81353613852-0.7531039710030.110417006882-0.0533600026222-1.086338787280.552545061267-1.39837897472-0.6871674010010.1923259628860.2126991956871.13426818366-0.03229477962940.04587144096890.527017244247-0.02103254209910.73847303940513.215973018243.038405231277.1971848273
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 233 )AA1 - 2331 - 220
22chain 'A' and (resid 234 through 295 )AA234 - 295221 - 282
33chain 'A' and (resid 296 through 415 )AA296 - 415283 - 402
44chain 'B' and (resid 1 through 233 )BB1 - 2331 - 223
55chain 'B' and (resid 234 through 295 )BB234 - 295224 - 285
66chain 'B' and (resid 296 through 414 )BB296 - 414286 - 404

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