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- PDB-1k1b: Crystal structure of the ankyrin repeat domain of Bcl-3: a unique... -

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Basic information

Entry
Database: PDB / ID: 1k1b
TitleCrystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family
ComponentsB-cell lymphoma 3-encoded protein
KeywordsTRANSCRIPTION / Bcl-3 / NF-kappaB transcription factors / IkappaB proteins
Function / homology
Function and homology information


Bcl3-Bcl10 complex / follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / regulation of DNA binding / marginal zone B cell differentiation / regulation of non-canonical NF-kappaB signal transduction / T cell apoptotic process / negative regulation of interleukin-8 production / germinal center formation / negative regulation of receptor signaling pathway via JAK-STAT ...Bcl3-Bcl10 complex / follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / regulation of DNA binding / marginal zone B cell differentiation / regulation of non-canonical NF-kappaB signal transduction / T cell apoptotic process / negative regulation of interleukin-8 production / germinal center formation / negative regulation of receptor signaling pathway via JAK-STAT / humoral immune response mediated by circulating immunoglobulin / negative regulation of T cell apoptotic process / antimicrobial humoral response / T-helper 2 cell differentiation / response to UV-C / T-helper 1 type immune response / negative regulation of NF-kappaB transcription factor activity / defense response to protozoan / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / DNA damage response, signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / spleen development / extracellular matrix organization / positive regulation of translation / response to virus / protein import into nucleus / histone deacetylase binding / transcription corepressor activity / positive regulation of type II interferon production / protein-macromolecule adaptor activity / midbody / regulation of apoptotic process / DNA-binding transcription factor binding / transcription coactivator activity / defense response to bacterium / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA damage response / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
B-cell lymphoma 3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMichel, F. / Soler-Lopez, M. / Petosa, C. / Cramer, P. / Siebenlist, U. / Mueller, C.W.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family.
Authors: Michel, F. / Soler-Lopez, M. / Petosa, C. / Cramer, P. / Siebenlist, U. / Muller, C.W.
History
DepositionSep 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell lymphoma 3-encoded protein


Theoretical massNumber of molelcules
Total (without water)25,8291
Polymers25,8291
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.350, 50.907, 59.495
Angle α, β, γ (deg.)90.00, 102.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein B-cell lymphoma 3-encoded protein / BCL3 / BCL-3 protein


Mass: 25829.451 Da / Num. of mol.: 1 / Fragment: ANKYRIN REPEAT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20749
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.8 Å3/Da / Density % sol: 31.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMMES1drop
2350 mM1dropNaCl
35 mMdithiothreitol1drop
43-10 mg/mlprotein1drop
55 %PEG60001reservoir
6100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 14381 / Num. obs: 14381 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.41 % / Rsym value: 0.097 / Net I/σ(I): 15.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.68 % / Mean I/σ(I) obs: 3.15 / Num. unique all: 1378 / Rsym value: 0.26 / % possible all: 94.4
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 49074 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 94.4 % / Rmerge(I) obs: 0.26

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ikn

1ikn


Resolution: 1.9→20 Å / SU B: 3.61543 / SU ML: 0.10851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19561 / ESU R Free: 0.15851 / Stereochemistry target values: Engh & Huber
Details: RESIDUES LEU182 AND SER307 PRESENT DOUBLE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21673 709 5 %RANDOM
Rwork0.17672 ---
all0.1787 14542 --
obs0.1787 14542 97.6 %-
Displacement parametersBiso mean: 19.188 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å21.17 Å2
2---1.18 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 0 198 1915
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.021
X-RAY DIFFRACTIONp_mcbond_it0.491.5
X-RAY DIFFRACTIONp_mcangle_it0.9252
X-RAY DIFFRACTIONp_scbond_it1.5033
X-RAY DIFFRACTIONp_scangle_it2.5334.5
X-RAY DIFFRACTIONp_plane_restr0.0040.02
X-RAY DIFFRACTIONp_chiral_restr0.0910.2
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1

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