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- PDB-4j19: Structure of a novel telomere repeat binding protein bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4j19
TitleStructure of a novel telomere repeat binding protein bound to DNA
Components
  • DNA (5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*A)-3')
  • Homeobox-containing protein 1
KeywordsTranscription/DNA / telomere repeat binding / telomeric DNA / Transcription-DNA complex
Function / homology
Function and homology information


regulation of telomerase activity / double-stranded telomeric DNA binding / positive regulation of chromatin binding / telomeric DNA binding / Cajal body / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / PML body / sequence-specific double-stranded DNA binding / sequence-specific DNA binding ...regulation of telomerase activity / double-stranded telomeric DNA binding / positive regulation of chromatin binding / telomeric DNA binding / Cajal body / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / PML body / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromosome, telomeric region / nuclear body / negative regulation of DNA-templated transcription / centrosome / chromatin / protein-containing complex binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Homeobox-containing protein 1 / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...Homeobox-containing protein 1 / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Homeobox-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Lopes Novo, C. / Basquin, C. / Krastev, D.B. / Kittler, R. ...Kappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Lopes Novo, C. / Basquin, C. / Krastev, D.B. / Kittler, R. / Jessberger, R. / Londono-Vallejo, A.J. / Mann, M. / Buchholz, F.
CitationJournal: Embo J. / Year: 2013
Title: HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment.
Authors: Kappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Novo, C.L. / Basquin, C. / Araki, M. / Araki, K. / Krastev, D.B. / Kittler, R. / Jessberger, R. / Londono- ...Authors: Kappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Novo, C.L. / Basquin, C. / Araki, M. / Araki, K. / Krastev, D.B. / Kittler, R. / Jessberger, R. / Londono-Vallejo, J.A. / Mann, M. / Buchholz, F.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox-containing protein 1
B: Homeobox-containing protein 1
C: DNA (5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
D: DNA (5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8665
Polymers37,8304
Non-polymers351
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.433, 116.490, 75.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

#1: Protein Homeobox-containing protein 1


Mass: 13102.929 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 233-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMBOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NT76
#2: DNA chain DNA (5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Mass: 5946.842 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*A)-3')


Mass: 5677.716 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 24% PEG 3350, 100 mM sodium acetate, 100 mM potassium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→46.155 Å / Num. obs: 11682 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: dev_1218)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CUF

2cuf


Resolution: 2.9→46.155 Å / SU ML: 0.4 / σ(F): 2.01 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 556 4.96 %
Rwork0.1718 --
obs0.1741 11682 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 769 1 66 2066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052114
X-RAY DIFFRACTIONf_angle_d0.9893014
X-RAY DIFFRACTIONf_dihedral_angle_d24.244840
X-RAY DIFFRACTIONf_chiral_restr0.043326
X-RAY DIFFRACTIONf_plane_restr0.003261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.05280.37331290.31822686X-RAY DIFFRACTION94
3.0528-3.2440.33041400.26512758X-RAY DIFFRACTION96
3.244-3.49440.24071490.18972739X-RAY DIFFRACTION96
3.4944-3.84590.221410.17162759X-RAY DIFFRACTION96
3.8459-4.4020.23181440.15362712X-RAY DIFFRACTION95
4.402-5.54460.15821510.15842706X-RAY DIFFRACTION94
5.5446-46.1550.22551420.15342718X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 23.6493 Å / Origin y: 28.3987 Å / Origin z: 13.206 Å
111213212223313233
T0.5031 Å20.0331 Å20.03 Å2-0.5137 Å20.0107 Å2--0.4789 Å2
L3.4277 °21.9456 °2-0.6289 °2-1.6589 °2-0.8966 °2--2.4369 °2
S0.0381 Å °-0.0959 Å °-0.005 Å °0.1242 Å °-0.0743 Å °-0.1767 Å °-0.4141 Å °0.1924 Å °0.0149 Å °
Refinement TLS groupSelection details: all

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