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- PDB-1lky: Structure of the wild-type TEL-SAM polymer -

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Basic information

Entry
Database: PDB / ID: 1lky
TitleStructure of the wild-type TEL-SAM polymer
Components(TRANSCRIPTION FACTOR ETV6) x 2
KeywordsTRANSCRIPTION / leukemia / tyrosine kinase / transcriptional repression / drug design
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / 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 / Signaling by FLT3 fusion proteins / neurogenesis / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin / regulation of transcription by RNA polymerase II / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTran, H.H. / Kim, C.A. / Faham, S. / Bowie, J.U.
CitationJournal: BMC STRUCT.BIOL. / Year: 2002
Title: Native interface of the SAM domain polymer of TEL.
Authors: Tran, H.H. / Kim, C.A.
History
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR ETV6
B: TRANSCRIPTION FACTOR ETV6
C: TRANSCRIPTION FACTOR ETV6
D: TRANSCRIPTION FACTOR ETV6
E: TRANSCRIPTION FACTOR ETV6
F: TRANSCRIPTION FACTOR ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69817
Polymers55,6416
Non-polymers1,05711
Water2,378132
1
A: TRANSCRIPTION FACTOR ETV6
B: TRANSCRIPTION FACTOR ETV6
hetero molecules

C: TRANSCRIPTION FACTOR ETV6
D: TRANSCRIPTION FACTOR ETV6
hetero molecules

E: TRANSCRIPTION FACTOR ETV6
F: TRANSCRIPTION FACTOR ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69817
Polymers55,6416
Non-polymers1,05711
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_444x-1,y-1,z-11
Buried area8440 Å2
ΔGint-162 kcal/mol
Surface area23620 Å2
MethodPISA
2
E: TRANSCRIPTION FACTOR ETV6
F: TRANSCRIPTION FACTOR ETV6
hetero molecules

A: TRANSCRIPTION FACTOR ETV6
B: TRANSCRIPTION FACTOR ETV6
C: TRANSCRIPTION FACTOR ETV6
D: TRANSCRIPTION FACTOR ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69817
Polymers55,6416
Non-polymers1,05711
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_454x-1,y,z-11
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-174 kcal/mol
Surface area22850 Å2
MethodPISA
3
E: TRANSCRIPTION FACTOR ETV6
F: TRANSCRIPTION FACTOR ETV6
hetero molecules

A: TRANSCRIPTION FACTOR ETV6
B: TRANSCRIPTION FACTOR ETV6
C: TRANSCRIPTION FACTOR ETV6
D: TRANSCRIPTION FACTOR ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69817
Polymers55,6416
Non-polymers1,05711
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_444x-1,y-1,z-11
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-167 kcal/mol
Surface area23790 Å2
MethodPISA
4
E: TRANSCRIPTION FACTOR ETV6
F: TRANSCRIPTION FACTOR ETV6
hetero molecules

C: TRANSCRIPTION FACTOR ETV6
D: TRANSCRIPTION FACTOR ETV6
hetero molecules

A: TRANSCRIPTION FACTOR ETV6
B: TRANSCRIPTION FACTOR ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69817
Polymers55,6416
Non-polymers1,05711
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area7660 Å2
ΔGint-145 kcal/mol
Surface area24400 Å2
MethodPISA
5
A: TRANSCRIPTION FACTOR ETV6
B: TRANSCRIPTION FACTOR ETV6
hetero molecules

C: TRANSCRIPTION FACTOR ETV6
D: TRANSCRIPTION FACTOR ETV6
hetero molecules

E: TRANSCRIPTION FACTOR ETV6
F: TRANSCRIPTION FACTOR ETV6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69817
Polymers55,6416
Non-polymers1,05711
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area8110 Å2
ΔGint-154 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.752, 60.291, 62.318
Angle α, β, γ (deg.)116.21, 98.89, 98.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TRANSCRIPTION FACTOR ETV6 / TEL SAM


Mass: 9280.590 Da / Num. of mol.: 3 / Fragment: Pointed domain / Mutation: V80R
Source method: isolated from a genetically manipulated source
Details: mutant V80R / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P41212
#2: Protein TRANSCRIPTION FACTOR ETV6 / TEL SAM


Mass: 9266.538 Da / Num. of mol.: 3 / Fragment: Pointed domain / Mutation: A61D
Source method: isolated from a genetically manipulated source
Details: mutant A61D / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P41212
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% PEG 4000 2.0 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
210 mMBis-Tris propane1droppH8.5
3200 mM1dropNaCl
45 %PEG40001reservoir
52.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2001
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 53910 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.3→2.38 Å / % possible all: 95.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 500 Å
Reflection shell
*PLUS
% possible obs: 95.6 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1JI7

1ji7


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2582 9.9 %RANDOM
Rwork0.232 ---
obs0.232 26185 89.3 %-
all-26185 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.7932 Å2 / ksol: 0.363415 e/Å3
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1-21.61 Å2-6.88 Å2-8.49 Å2
2---11.11 Å2-2.19 Å2
3----10.5 Å2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 55 132 4096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 381 10.1 %
Rwork0.347 3396 -
obs--77.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE_HEX.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4ION.PARAM
Refinement
*PLUS
Lowest resolution: 500 Å / % reflection Rfree: 10 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor obs: 0.347

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