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- PDB-1lei: The kB DNA sequence from the HLV-LTR functions as an allosteric r... -

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Basic information

Entry
Database: PDB / ID: 1lei
TitleThe kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription
Components
  • 5'-D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3'
  • 5'-D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP*G)-3'
  • NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT
  • NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
KeywordsTRANSCRIPTION/DNA / transcription factor / NF-kB-DNA complex / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process ...cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / antibacterial innate immune response / positive regulation of chondrocyte differentiation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / prolactin signaling pathway / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / cellular response to peptide / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / cellular response to dsRNA / negative regulation of interleukin-12 production / ankyrin repeat binding / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / nucleotide-binding oligomerization domain containing 2 signaling pathway / actinin binding / cellular response to angiotensin / negative regulation of non-canonical NF-kappaB signal transduction / response to UV-B / NF-kappaB complex / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / vascular endothelial growth factor signaling pathway / negative regulation of cytokine production / toll-like receptor 4 signaling pathway / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / cellular response to organic cyclic compound / response to muramyl dipeptide / general transcription initiation factor binding / cellular response to interleukin-1 / NF-kappaB binding / positive regulation of vascular endothelial growth factor production / hair follicle development / neuropeptide signaling pathway / response to amino acid / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / lymph node development / canonical NF-kappaB signal transduction / JNK cascade / heat shock protein binding / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to cAMP / cellular response to brain-derived neurotrophic factor stimulus / response to muscle stretch / positive regulation of interleukin-12 production / Neutrophil degranulation / negative regulation of angiogenesis / liver development / negative regulation of miRNA transcription / response to cytokine / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / response to bacterium / transcription coregulator activity / peptide binding / response to insulin / protein catabolic process / negative regulation of protein catabolic process / response to organic cyclic compound / chromatin DNA binding / cellular response to virus
Similarity search - Function
Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / Transcription factor RelA (p65) / 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 domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / Transcription factor RelA (p65) / 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 / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen-Park, F. / Huang, D.B. / Ghosh, G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The kB DNA sequence from the HIV Long Terminal Repeat functions as an allosteric regulator of HIV transcription
Authors: Chen-Park, F.E. / Huang, D.B. / Noro, B. / Thanos, D. / Ghosh, G.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / struct_ref_seq_dif
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
Revision 1.4Sep 20, 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
C: 5'-D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3'
D: 5'-D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP*G)-3'
A: NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
B: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)77,0334
Polymers77,0334
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.131, 179.697, 97.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: DNA chain 5'-D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3'


Mass: 5269.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: kB DNA
#2: DNA chain 5'-D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP*G)-3'


Mass: 5591.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: kB DNA
#3: Protein NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT / NF-kB p65


Mass: 31115.236 Da / Num. of mol.: 1 / Fragment: p65 RHR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: rela / Plasmid: ET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04207
#4: Protein NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT / NF-kB p50


Mass: 35056.066 Da / Num. of mol.: 1 / Fragment: p50 RHR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: nfkb1 / Plasmid: ET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25799
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 291 K / Method: small tubes / pH: 6.5
Details: PEG 3350, CaCl2, sodium spermine, pH 6.5, SMALL TUBES, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2CaCl211
3sodium spermine11
4CaCl212
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
250 mMsodium MES1reservoirpH6.5
3200 mM1reservoirCaCl2
40.05 %beta-octyl glucopyranoside1reservoir
50.05 mMsodium spermine1reservoir
610 mMdithiothreitol1reservoir
710 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 1999
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 33470 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.8
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / % possible all: 89
Reflection
*PLUS
% possible obs: 98 % / Num. measured all: 254045
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.315

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKX

1vkx


Resolution: 2.7→20 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1525 -RANDOM
Rwork0.25 ---
obs-29985 87.1 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 691 0 23 5344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_bond_d0.007
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0072

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