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- PDB-1ji7: Crystal Structure of TEL SAM Polymer -

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Basic information

Entry
Database: PDB / ID: 1ji7
TitleCrystal Structure of TEL SAM Polymer
ComponentsETS-RELATED PROTEIN TEL1
KeywordsTRANSCRIPTION / Helical 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 / 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 / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsKim, C.A. / Phillips, M.L. / Kim, W. / Gingery, M. / Tran, H.H. / Robinson, M.A. / Faham, S. / Bowie, J.U.
CitationJournal: EMBO J. / Year: 2001
Title: Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression.
Authors: Kim, C.A. / Phillips, M.L. / Kim, W. / Gingery, M. / Tran, H.H. / Robinson, M.A. / Faham, S. / Bowie, J.U.
History
DepositionJun 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ETS-RELATED PROTEIN TEL1
B: ETS-RELATED PROTEIN TEL1
C: ETS-RELATED PROTEIN TEL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3288
Polymers32,8473
Non-polymers4805
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.865, 52.678, 58.701
Angle α, β, γ (deg.)90.00, 113.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ETS-RELATED PROTEIN TEL1 / TRANSCRIPTION FACTOR ETV6


Mass: 10949.143 Da / Num. of mol.: 3 / Fragment: TEL SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEL / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P41212
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Li2SO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
210 mMTris1droppH8.5
3200 mM1dropNaCl
450 mMTris1reservoirpH8.0
51.6 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.978803, 0.971349, 0.979018
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9788031
20.9713491
30.9790181
ReflectionResolution: 1.45→19.9 Å / Num. all: 244968 / Num. obs: 139887 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.2
Reflection shellResolution: 1.45→1.51 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.282 / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 244968 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.45 Å / % possible obs: 97.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.45→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1312800.12 / Data cutoff high rms absF: 1312800.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 6265 10.1 %RANDOM
Rwork0.184 ---
obs-61824 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.96 Å2 / ksol: 0.423 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.03 Å2
2--3.51 Å20 Å2
3----2.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 25 242 2347
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.45-1.50.2298569100.20988566505886
1.5-1.560.20525770.1938528389
1.56-1.630.19266060.1781545192
1.63-1.720.19956550.1753546293
1.72-1.830.20216080.1781563395
1.83-1.970.18386450.1676568497
1.97-2.170.19286820.1746575398
2.17-2.480.1866400.1785579598
2.48-3.120.20146260.1869579597
3.12-5000.19276570.1918564593
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.45 Å / Rfactor Rfree: 0.2298 / Rfactor Rwork: 0.2098

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