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- PDB-6ptl: Structure of the self-association domain of the chromatin looping... -

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Basic information

Entry
Database: PDB / ID: 6ptl
TitleStructure of the self-association domain of the chromatin looping factor LDB1
ComponentsLIM domain-binding protein 1
KeywordsGENE REGULATION / Dimer / Chromatin looping factor / nuclear protein / transcriptional regulator
Function / homology
Function and homology information


regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / primitive erythrocyte differentiation / head development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / beta-catenin-TCF complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs ...regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / primitive erythrocyte differentiation / head development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / beta-catenin-TCF complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / epithelial structure maintenance / LIM domain binding / gastrulation with mouth forming second / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / hair follicle development / regulation of cell migration / positive regulation of cell adhesion / cerebellum development / positive regulation of transcription elongation by RNA polymerase II / neuron differentiation / Wnt signaling pathway / RNA polymerase II transcription regulator complex / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile.
Similarity search - Domain/homology
LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMacindoe, I. / Silva, A. / Guss, J.M. / Mackay, J.P. / Matthews, J.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1064442 Australia
Australian Research Council (ARC)DP190102543 Australia
CitationJournal: To Be Published
Title: Structure of the self-association domain of the chromatin looping factor LDB1
Authors: Macindoe, I. / Silva, A. / Guss, J.M. / Mackay, J.P. / Matthews, J.M.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIM domain-binding protein 1


Theoretical massNumber of molelcules
Total (without water)22,6081
Polymers22,6081
Non-polymers00
Water1629
1
A: LIM domain-binding protein 1

A: LIM domain-binding protein 1


  • defined by author&software
  • Evidence: light scattering, Under concentrations tested, MALLS analysis indicates a dimer is the main species in solution, SAXS, Supports major species being dimer. Crysol modelling indicates that a ...Evidence: light scattering, Under concentrations tested, MALLS analysis indicates a dimer is the main species in solution, SAXS, Supports major species being dimer. Crysol modelling indicates that a dimer with the major interface is the most likely species in solution. Some evidence of concentration dependent higher order association at higher concentrations., cross-linking, Analysed by mass spectrometry supports the main interface, mass spectrometry, Native mass spectrometry indicates that dimer is the most prevalent multimeric species
  • 45.2 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)45,2152
Polymers45,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2280 Å2
ΔGint-10 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.869, 81.869, 66.828
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LIM domain-binding protein 1 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / ...LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / mLdb1 / Nuclear LIM interactor


Mass: 22607.703 Da / Num. of mol.: 1 / Fragment: UNP residues 50-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldb1, Nli / Plasmid: pHIS-GB1
Details (production host): T7 regulated expression with a His tag for purification and a GB1 tag to enhance soluble expression
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70662
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8656.99
22.8656.99
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting drop18.6% PEG3350, 140 mM sodium phosphate dibasic
2932vapor diffusion, sitting drop18.6% PEG3350, 140 mM sodium phosphate dibasic, crystal soaked overnight in mother liquor containing 10 mM ethylmercury thiosalicylic acid

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX210.9537
SYNCHROTRONAustralian Synchrotron MX120.9537
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDSep 27, 2014
ADSC QUANTUM 210r2CCDFeb 28, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2double crystal Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21
Reflection

Entry-ID: 6PTL

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allΧ2Diffraction-IDNet I/σ(I)
2.5-35.5921299.710.775.20.9980.0830.0270.0871.01114.7
2.8-501252399.911.697.60.9940.0950.0320.1071.3215.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.6111.2132.510150.9290.3811.2711.07100
2.8-2.8511.61.4741.46680.60.6632.2561.354100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-20002.3.12data reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.32 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.26
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 496 5.4 %RANDOM
Rwork0.2448 ---
obs0.2463 8696 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.85 Å2 / Biso mean: 87.291 Å2 / Biso min: 64.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å21.14 Å20 Å2
2--2.28 Å2-0 Å2
3----7.41 Å2
Refinement stepCycle: final / Resolution: 2.5→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 0 9 1222
Biso mean---81.32 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0131257
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171118
X-RAY DIFFRACTIONr_angle_refined_deg1.141.6561696
X-RAY DIFFRACTIONr_angle_other_deg1.0131.5772583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.68520.84383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2341512
X-RAY DIFFRACTIONr_chiral_restr0.0320.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
LS refinement shellResolution: 2.502→2.567 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 20 -
Rwork0.347 669 -
all-689 -
obs--100 %

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