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- PDB-1gji: Crystal structure of c-Rel bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1gji
TitleCrystal structure of c-Rel bound to DNA
Components
  • (IL-2 CD28RE DNA) x 2
  • C-REL PROTO-ONCOGENE PROTEIN
KeywordsTRANSCRIPTION/DNA / NF-kB-DNA COMPLEX / TRANSCRIPTION FACTOR / c-Rel HOMODIMER / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


apoptotic DNA fragmentation / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / DNA-binding transcription factor activity / innate immune response / chromatin binding ...apoptotic DNA fragmentation / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / DNA-binding transcription factor activity / innate immune response / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Proto-oncogene c-Rel / Proto-oncogene c-Rel, RHD, N-terminal subdomain / Rel homology domain (RHD), DNA-binding domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain ...Proto-oncogene c-Rel / Proto-oncogene c-Rel, RHD, N-terminal subdomain / Rel homology domain (RHD), DNA-binding domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Proto-oncogene c-Rel
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / molecular replacement, MIR / Resolution: 2.85 Å
AuthorsHuang, D.B. / Chen, Y.Q. / Ruetsche, M. / Phelps, C.B. / Ghosh, G.
CitationJournal: Structure / Year: 2001
Title: X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2.
Authors: Huang, D.B. / Chen, Y.Q. / Ruetsche, M. / Phelps, C.B. / Ghosh, G.
History
DepositionMay 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: IL-2 CD28RE DNA
D: IL-2 CD28RE DNA
A: C-REL PROTO-ONCOGENE PROTEIN
B: C-REL PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)76,0544
Polymers76,0544
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.320, 99.320, 196.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain IL-2 CD28RE DNA


Mass: 6206.054 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain IL-2 CD28RE DNA


Mass: 6058.939 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein C-REL PROTO-ONCOGENE PROTEIN / C-REL PROTEIN


Mass: 31894.316 Da / Num. of mol.: 2 / Fragment: Rel homology region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P16236

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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: 3.16 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: PEG 4000, spermine, DTT, pH 7.5, EVAPORATION, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2spermine11
3DTT11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 %(w/v)PEG40001reservoir
3100 mMHEPES1reservoirpH7.5
41 mMspermine1reservoir
52 mMdithiothreitol1reservoir
60.01 %beta-octylglucoside1reservoir

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Data collection

DiffractionMean temperature: 168 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Feb 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→25 Å / Num. all: 21455 / Num. obs: 18723 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.8
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 7 % / Rmerge(I) obs: 0.424 / Num. unique all: 1159 / % possible all: 46
Reflection
*PLUS
Num. obs: 21455 / % possible obs: 90 % / Num. measured all: 215187 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 48 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement, MIR
Starting model: p65/DNA complex

Resolution: 2.85→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The DNA molecule has alternate conformations. Two sets of coordinates for the DNA molecule were refined with 0.5 occupancy each.
RfactorNum. reflection% reflection
Rfree0.279 897 5 %
Rwork0.227 --
all-21455 -
obs-18732 79.2 %
Refinement stepCycle: LAST / Resolution: 2.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 1628 0 0 6114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.32
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.227 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0079

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